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Crystal structure of the VEL1 VEL polymerising domain (R643A K645D I664D mutant)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 20% PEG 3350, 2M Sodium malonate pH7
Crystal Properties Matthews coefficient Solvent content 2.77 55.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.066 α = 90 b = 58.053 β = 90 c = 119.991 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS3 6M 2020-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.979500 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.5 29.04 100 0.99 9.6 20 13183
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 0.84
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 (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 2.5 29.04 13134 649 99.92 0.21492 0.21358 0.2263 0.2407 0.245 RANDOM 64.134
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] 4.14 -1.2 -2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.843 r_dihedral_angle_4_deg 20.241 r_dihedral_angle_3_deg 14.247 r_dihedral_angle_1_deg 4.386 r_long_range_B_refined 2.115 r_long_range_B_other 2.114 r_scangle_other 1.384 r_mcangle_it 1.275 r_mcangle_other 1.274 r_angle_refined_deg 1.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.843 r_dihedral_angle_4_deg 20.241 r_dihedral_angle_3_deg 14.247 r_dihedral_angle_1_deg 4.386 r_long_range_B_refined 2.115 r_long_range_B_other 2.114 r_scangle_other 1.384 r_mcangle_it 1.275 r_mcangle_other 1.274 r_angle_refined_deg 1.157 r_angle_other_deg 1.102 r_scbond_it 0.818 r_scbond_other 0.818 r_mcbond_it 0.766 r_mcbond_other 0.766 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2293 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling CRANK2 phasing Coot model building PDB_EXTRACT data extraction