Experiment: 5DMI

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JMA	CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X
experimental model	PDB	2UWI	CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X
experimental model	PDB	2AW2	CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X
experimental model	PDB	1NCF	CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X
experimental model	PDB	1TNR	CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X
experimental model	PDB	2HEV	CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X
experimental model	PDB	2HEY	CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X
experimental model	PDB	3D85	CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X
experimental model	PDB	2ZPK	CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X
experimental model	PDB	2O5X	CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	80mM sodiym acetate, pH 4.6, 1.6 M ammonium sulfate, 20% (v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
4.8	74

Crystal Data

Unit Cell
Length ( ? )	Angle ( ? )
a = 201.152	�� = 90
b = 201.152	�� = 90
c = 63.809	�� = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX-225		2010-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.69	201.15	100	0.249	13.2	15.9		14668			11.33

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.69	3.89	100		0.495	6.8	16.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X	3.69	32.64	14605	734	99.77	0.1702	0.1683	0.18	0.207	0.22	RANDOM	42.89

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-8.9003			-8.9003		17.8005

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	25.24
t_omega_torsion	3.18
t_angle_deg	1.39
t_bond_d	0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	25.24
t_omega_torsion	3.18
t_angle_deg	1.39
t_bond_d	0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4001
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	10

Software

Software
Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.