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Disulfide deficient mutant of vascular endothelial growth factor A (C61A and C104A)
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 0.1701 0.19515 0.1696 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
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 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_xyhbond_nbd-refined r_symmetry_vdw_refined r_symmetry_hbond_refined
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