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Crystal Structure of the Orf Virus NZ2 Variant of VEGF-E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.6 M Ammonium sulfate, 3% PEG 4K, 0.1 M Sodium citrate, 0.3% Benzamidine, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 5.10419 75.902153
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.6 α = 90 b = 98.6 β = 90 c = 240 γ = 90
Symmetry Space Group P 41 2 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 MAR CCD 165 mm 2004-07-27 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MAR CCD 165 mm 2004-07-31 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00017 SLS X06SA 2 SYNCHROTRON SLS BEAMLINE X06SA 1.698383 SLS X06SA
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 1,2 2.3 48.48 93.4 0.081 14.58 52820 57.637
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) 1,2 2.3 2.4 98.4 85.4 0.799 3.1 6199
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 SAD THROUGHOUT 2.3 48.48 52820 2687 98.66 0.224 0.224 0.223 0.2109 0.247 0.2303 RANDOM 66.047
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] 1.93 1.93 -3.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.619 r_dihedral_angle_3_deg 15.601 r_dihedral_angle_4_deg 12.628 r_scangle_it 7.725 r_scbond_it 5.293 r_dihedral_angle_1_deg 5.052 r_mcangle_it 3.347 r_mcbond_it 2.075 r_angle_refined_deg 1.25 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.619 r_dihedral_angle_3_deg 15.601 r_dihedral_angle_4_deg 12.628 r_scangle_it 7.725 r_scbond_it 5.293 r_dihedral_angle_1_deg 5.052 r_mcangle_it 3.347 r_mcbond_it 2.075 r_angle_refined_deg 1.25 r_nbtor_refined 0.293 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.198 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2831 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 132
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection SHELXD phasing