3BDY | pdb_00003bdy

Dual specific bH1 Fab 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	1N8Z	PDB entry 1N8Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	292	For crystallization of the Fab/VEGF (8-109) complex, equal volumes of protein complex solution (10.6 mg/ml protein, 300 mM NaCl, 25 mM Tris-HCl pH 7.5) and crystallization buffer containing 0.15 D, L Malic Acid pH 7.0, 20% PEG3350 were mixed and equilibrated at 19 C. Prior to data collection the crystals were cryo-protected by transfer between drops containing 5%, 10% and 15% Glycerol in artificial mother liquor, followed by flash freeze in liquid nitrogen, VAPOR DIFFUSION, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.6	α = 90
b = 197.978	β = 90
c = 77.65	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 315		2006-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.00	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.6	50	99.8	0.09	16	6.2	24755	24705

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.69	100		0.658	3	6.2	2419

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1N8Z	2.6	30	24225	1248	99.81	0.197	0.194	0.19	0.252	0.25	RANDOM	40.479

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]
-1.01			-0.56		1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.833
r_dihedral_angle_4_deg	15.435
r_dihedral_angle_3_deg	15.219
r_dihedral_angle_1_deg	6.122
r_scangle_it	3.823
r_mcangle_it	3.645
r_mcbond_it	2.769
r_scbond_it	2.67
r_angle_refined_deg	1.255
r_angle_other_deg	0.805
r_mcbond_other	0.517
r_symmetry_vdw_refined	0.346
r_nbd_other	0.19
r_nbd_refined	0.185
r_nbtor_refined	0.181
r_symmetry_vdw_other	0.14
r_xyhbond_nbd_refined	0.127
r_nbtor_other	0.084
r_symmetry_hbond_refined	0.075
r_chiral_restr	0.072
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4072
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	6

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection