2FJH

Structure of the B20-4 Fab, a phage derived Fab fragment, in complex with VEGF

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FLT	Search model for VEGF was based on 1FLT, search model for Fab was based on 2FJF.
experimental model	PDB	2FJF	Search model for VEGF was based on 1FLT, search model for Fab was based on 2FJF.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	292	0.1 M Sodium acetate, 1.6 M Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
5.046684	75.627563

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 165.538	α = 90
b = 165.538	β = 90
c = 150.548	γ = 120

Symmetry
Space Group	P 31 1 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		2004-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.0	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.1	50	99.8			42840	42755

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.21	100

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	Search model for VEGF was based on 1FLT, search model for Fab was based on 2FJF.	3.1	30	42910	39869	2120	97.99	0.21	0.20038	0.19829	0.2394	RANDOM	55.043

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]
2.32	1.16		2.32		-3.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.786
r_scangle_it	6.163
r_mcangle_it	5.716
r_scbond_it	3.787
r_mcbond_it	3.34
r_angle_refined_deg	1.42
r_symmetry_vdw_refined	0.237
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.15
r_symmetry_hbond_refined	0.116
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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	8103
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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