3O2W | pdb_00003o2w

Crystal structure of the 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe Fab in complex with a 39A11 transition state analog

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		1E9 PheL89Ser/LeuH47Trp/MetH100bPhe Fab apo structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	2.25M ammoniumsulfate, 0.15M sodiumcitrate, 0.01% PEG20000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.51	72.7

Crystal Data

Unit Cell
Length ( ? )	Angle ( ? )
a = 128.203	�� = 90
b = 128.203	�� = 90
c = 92.144	�� = 120

Symmetry
Space Group	P 31 2 1

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	ADSC QUANTUM 210		2005-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.059658	ALS	8.2.1

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	2.55	50	98.6	0.071	14.6	4.1		28353

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.64	99.9		0.55	1.7

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	rigid body refinement	THROUGHOUT	1E9 PheL89Ser/LeuH47Trp/MetH100bPhe Fab apo structure	2.55	50	26768	1365	97.89	0.20907	0.20713	0.21	0.24825	0.25	RANDOM	79.982

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]
4.05	2.03		4.05		-6.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.272
r_dihedral_angle_4_deg	19.501
r_dihedral_angle_3_deg	18.02
r_dihedral_angle_1_deg	6.814
r_scangle_it	2.839
r_scbond_it	1.839
r_angle_refined_deg	1.74
r_mcangle_it	1.145
r_mcbond_it	0.656
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.272
r_dihedral_angle_4_deg	19.501
r_dihedral_angle_3_deg	18.02
r_dihedral_angle_1_deg	6.814
r_scangle_it	2.839
r_scbond_it	1.839
r_angle_refined_deg	1.74
r_mcangle_it	1.145
r_mcbond_it	0.656
r_nbtor_refined	0.315
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.166
r_symmetry_hbond_refined	0.134
r_chiral_restr	0.097
r_bond_refined_d	0.019
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3312
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	190

Software

Software
Software Name	Purpose
BOS	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	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.