☰ Navigation Tabs
Crystal structure of Cph001-D189N in complex with VIO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8I80
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 Sodium acetate trihydrate pH 4.6,
Polyethylene glycol 4,000,
Glycerol
Crystal Properties Matthews coefficient Solvent content 2.55 51.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.122 α = 90 b = 87.104 β = 90 c = 87.136 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 CCD RAYONIX MX300-HS 2022-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 1 NSRRC TPS 07A
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 30 99.8 0.053 36.5 7.8 43019
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 2.07 99.3 0.55 2.8 7.3
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 MOLECULAR REPLACEMENT THROUGHOUT 2 23.19 40916 2041 99.39 0.20706 0.20492 0.2138 0.25244 0.2602 RANDOM 44.965
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] 0.04 -4.53 4.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.314 r_dihedral_angle_1_deg 6.051 r_dihedral_angle_2_deg 5.69 r_long_range_B_refined 5.672 r_long_range_B_other 5.67 r_scangle_other 3.854 r_mcangle_it 3.312 r_mcangle_other 3.312 r_scbond_it 2.39 r_scbond_other 2.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.314 r_dihedral_angle_1_deg 6.051 r_dihedral_angle_2_deg 5.69 r_long_range_B_refined 5.672 r_long_range_B_other 5.67 r_scangle_other 3.854 r_mcangle_it 3.312 r_mcangle_other 3.312 r_scbond_it 2.39 r_scbond_other 2.389 r_mcbond_it 2.124 r_mcbond_other 2.123 r_angle_refined_deg 0.933 r_angle_other_deg 0.325 r_chiral_restr 0.043 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4271 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 14
Software Software Software Name Purpose SCALA data scaling REFMAC refinement HKL-2000 data reduction MOLREP phasing