1TZI

Crystal Structure of the Fab YADS2 Complexed with h-VEGF

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VPF	The VEGF is from pdb entry 1VPF. The Fab is from an in-house determined structure.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	292	LITHIUM CHLORIDE, PEG 6000, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.504	α = 90
b = 149.588	β = 90
c = 117.421	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC QUANTUM 4		2003-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.000	SSRL	BL9-2

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	2.8	50	97.3	0.076	0.076	18.7	4.8	21429	20861		-3

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	2.8	2.9	82.92		0.4	0.4	2.5	83.2	2110

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	The VEGF is from pdb entry 1VPF. The Fab is from an in-house determined structure.	2.8	20	21229	19702	1023	97.63	0.2197	0.2197	0.21786	0.25447	RANDOM	46.845

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]
-8.87			1.62		7.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.592
r_mcangle_it	5.231
r_scangle_it	4.696
r_mcbond_it	3.211
r_scbond_it	2.869
r_angle_refined_deg	1.334
r_angle_other_deg	0.945
r_symmetry_vdw_refined	0.342
r_nbd_other	0.224
r_symmetry_vdw_other	0.208
r_nbd_refined	0.203
r_symmetry_hbond_refined	0.175
r_xyhbond_nbd_refined	0.134
r_nbtor_other	0.086
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4077
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing