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Crystal structure of the VASH1-SVBP complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 293 19% PEG 3000, 0.1M Tris-HCl, 0.2M calcium chloride
Crystal Properties Matthews coefficient Solvent content 3.23 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.453 α = 90 b = 128.929 β = 90 c = 45.222 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS3 2M 2018-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 47.61 99.7 0.062 0.99 12.8 4.9 24696
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 51.8 1.538 0.518 1.1 4.9
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 2.1 47.61 23437 1259 99.48 0.19839 0.19751 0.2063 0.21428 0.2301 RANDOM 57.224
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] -0.58 -1.87 2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.311 r_dihedral_angle_4_deg 15.269 r_dihedral_angle_3_deg 13.722 r_long_range_B_other 6.616 r_long_range_B_refined 6.615 r_dihedral_angle_1_deg 6.264 r_scangle_other 4.841 r_scbond_it 3.213 r_scbond_other 3.213 r_mcangle_it 3.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.311 r_dihedral_angle_4_deg 15.269 r_dihedral_angle_3_deg 13.722 r_long_range_B_other 6.616 r_long_range_B_refined 6.615 r_dihedral_angle_1_deg 6.264 r_scangle_other 4.841 r_scbond_it 3.213 r_scbond_other 3.213 r_mcangle_it 3.039 r_mcangle_other 3.038 r_mcbond_it 2.153 r_mcbond_other 2.15 r_angle_refined_deg 1.22 r_angle_other_deg 1.115 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2228 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling CRANK2 phasing