2O5X | pdb_00002o5x

Crystal structure of 1E9 LeuH47Trp/ArgH100Trp, an engineered Diels-Alderase Fab with nM steroid-binding affinity

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1C1E	PDB entry 1C1E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	1.5 M ammonium sulfate, 0.15 M sodium citrate, 0.01% PEG 20000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

Crystal Properties
Matthews coefficient	Solvent content
4.54	72.89

Crystal Data

Unit Cell
Length ( ? )	Angle ( ? )
a = 127.573	�� = 90
b = 127.573	�� = 90
c = 91.928	�� = 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		2004-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.99996	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.05	50	99.6	0.082	8.2	15.6	4.1	54755	54536			37.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.29	100		0.525	52.5	2.4	3.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB entry 1C1E	2.05	50	51644	51412	2730	99.55	0.17945	0.17945	0.17812	0.18	0.20399	0.2	RANDOM	48.637

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]
1.77	0.89		1.77		-2.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.609
r_dihedral_angle_4_deg	17.66
r_dihedral_angle_3_deg	16.154
r_scangle_it	8.307
r_dihedral_angle_1_deg	6.538
r_scbond_it	6.004
r_mcangle_it	3.418
r_mcbond_it	2.215
r_angle_refined_deg	1.674
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.609
r_dihedral_angle_4_deg	17.66
r_dihedral_angle_3_deg	16.154
r_scangle_it	8.307
r_dihedral_angle_1_deg	6.538
r_scbond_it	6.004
r_mcangle_it	3.418
r_mcbond_it	2.215
r_angle_refined_deg	1.674
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.242
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.148
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.128
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3349
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	63

Software

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