1MKK | pdb_00001mkk

Disulfide deficient mutant of vascular endothelial growth factor A (C61A and C104A)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VPF	PDB ENTRY 2VPF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	isopropanol, PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.22	α = 90
b = 75.47	β = 97.25
c = 55.12	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH		2002-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.8423	EMBL/DESY, HAMBURG	BW7B

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	1.32	28	99.2	0.074	12.08	3.8	53321	53321		-3	22.06

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)
	1.32	1.35	99.5		0.375	2.48	3.17	3498

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 (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 2VPF	1.32	28	53318	53318	5264	100	0.16836	0.16836	0.16543	0.17	0.19515	0.17	Resolution shells	19.583

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]
1.32		0.03	-0.86		-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.099
r_sphericity_free	13.105
r_sphericity_bonded	7.144
r_scangle_it	6.79
r_scbond_it	4.722
r_dihedral_angle_1_deg	4.432
r_mcangle_it	4.298
r_mcbond_it	2.959
r_rigid_bond_restr	2.331
r_angle_refined_deg	1.403

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1528
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345	data collection
XDS	data reduction
AMoRE	phasing
REFMAC	refinement
XDS	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.