3C7Q | pdb_00003c7q

Structure of VEGFR2 kinase domain in complex with BIBF1120

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VR2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	277	0.1M HEPES, 2.1M Ammonium Sulphate, 3% PEG MME 550, 10mM Beta-Mercaptoethanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.25	α = 90
b = 94.44	β = 90
c = 96.22	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	MARMOSAIC 225 mm CCD		2006-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9799	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	30	98.4	0.087	9.91			23933		-3	32.839

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	2	2.1	91.2		0.559	2

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 (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	1VR2	2.1	28.54	19934	19934	1050	100	0.221	0.217	0.22	0.279	0.28	RANDOM	24.366

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]
-0.87			2.84		-1.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.284
r_dihedral_angle_4_deg	17.038
r_dihedral_angle_3_deg	16.389
r_dihedral_angle_1_deg	8.311
r_scangle_it	2.529
r_scbond_it	1.789
r_angle_refined_deg	1.633
r_mcangle_it	1.354
r_mcbond_it	1.184
r_angle_other_deg	0.997
r_symmetry_hbond_refined	0.267
r_symmetry_vdw_other	0.22
r_nbd_refined	0.206
r_nbd_other	0.2
r_symmetry_vdw_refined	0.197
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.181
r_mcbond_other	0.155
r_chiral_restr	0.114
r_nbtor_other	0.089
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2362
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	65

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction