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Crystal structure of Cph001-D189N in complex with VIO and ATP
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,
Polyethylene glycol 4,000,
Glycerol
Crystal Properties Matthews coefficient Solvent content 2.6 52.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.144 α = 90 b = 87.364 β = 90 c = 88.41 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 2022-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
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 2.02 30 99.4 0.083 10.4 3.9 40292
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 2.02 2.14 98.1 0.584 2.4 4
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 2.02 29.08 40292 1996 99.52 0.22013 0.21848 0.2261 0.25197 0.2547 RANDOM 41.29
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] -0.08 0.1 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.37 r_dihedral_angle_3_deg 15.923 r_long_range_B_refined 8.059 r_long_range_B_other 8.058 r_dihedral_angle_1_deg 6.139 r_scangle_other 6.139 r_mcangle_other 4.738 r_mcangle_it 4.701 r_scbond_it 4.124 r_scbond_other 4.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.37 r_dihedral_angle_3_deg 15.923 r_long_range_B_refined 8.059 r_long_range_B_other 8.058 r_dihedral_angle_1_deg 6.139 r_scangle_other 6.139 r_mcangle_other 4.738 r_mcangle_it 4.701 r_scbond_it 4.124 r_scbond_other 4.123 r_mcbond_other 3.301 r_mcbond_it 3.217 r_angle_refined_deg 1.422 r_angle_other_deg 0.848 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 0.002 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 155 Heterogen Atoms 38
Software Software Software Name Purpose SCALA data scaling REFMAC refinement HKL-2000 data reduction MOLREP phasing