7KF0

Crystal structure of bH1 Fab variant (CDR H3 loop design 13_0346) in complex with VEGF

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		295	0.2 M Sodium acetate, 0.1 M HEPES pH 7.5, 20 %(w/v) PEG 3000

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.459	α = 90
b = 99.409	β = 90
c = 191.219	γ = 90

Symmetry
Space Group	P 21 21 21

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-300		2018-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.32	95.61	99.7	0.089	0.1	0.045	0.996	10	4.9		63680

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.32	2.38	99.9		0.742	0.834	0.37	0.685		5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3BDY	2.32	95.61	60457	3148	99.54	0.195	0.1924	0.2462	RANDOM	47.766

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]
0.79			1.8		-2.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.955
r_dihedral_angle_4_deg	25.885
r_dihedral_angle_3_deg	18.42
r_dihedral_angle_1_deg	7.006
r_angle_refined_deg	1.83
r_angle_other_deg	1.279
r_chiral_restr	0.101
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.955
r_dihedral_angle_4_deg	25.885
r_dihedral_angle_3_deg	18.42
r_dihedral_angle_1_deg	7.006
r_angle_refined_deg	1.83
r_angle_other_deg	1.279
r_chiral_restr	0.101
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8165
Nucleic Acid Atoms
Solvent Atoms	486
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	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 R01GM133198.