3HNG

Crystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.2M potassium formate, 20% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.04	α = 90
b = 71.15	β = 90
c = 196.02	γ = 90

Symmetry
Space Group	I 2 2 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	ADSC QUANTUM 4	TOROIDAL ZERODUR MIRROR	2009-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.93300	ESRF	ID14-2

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	2.7	44.99	99.8	0.088	0.078	13.2	4.7	11982	11958			65.8

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	2.67	2.81	98.5		0.506	0.441	3.2	4.2	1669

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2QU5	2.7	44.99	11021	10998	551	99.79	0.19739	0.19739	0.19431	0.26018	RANDOM	26.129

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]
0.09			1.14		-1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.976
r_dihedral_angle_4_deg	20.508
r_dihedral_angle_3_deg	19.825
r_dihedral_angle_1_deg	7.077
r_scangle_it	2.727
r_scbond_it	1.584
r_angle_refined_deg	1.46
r_mcangle_it	1.086
r_angle_other_deg	0.64
r_mcbond_it	0.547

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.976
r_dihedral_angle_4_deg	20.508
r_dihedral_angle_3_deg	19.825
r_dihedral_angle_1_deg	7.077
r_scangle_it	2.727
r_scbond_it	1.584
r_angle_refined_deg	1.46
r_mcangle_it	1.086
r_angle_other_deg	0.64
r_mcbond_it	0.547
r_mcbond_other	0.094
r_chiral_restr	0.073
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2290
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	25

Software

Software
Software Name	Purpose
ADSC	data collection
PHENIX	model building
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.