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SARS-CoV-2 papain-like protease (PLpro) bound to PF-07957472
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CMD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 30% v/v Jeffamine ED-2001 pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.866 α = 90 b = 99.662 β = 90 c = 188.682 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 EIGER2 X 16M 2023-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.95374 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.59 68.51 73.8 0.055 0.993 7.75 13.4 30611
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.69 52.2 0.82 0.976 13.7
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 2.595 45.15 30611 1482 79.2 0.236 0.2348 0.235 0.259 0.2537 RANDOM 71.62
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] -0.4182 -0.7757 1.194
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.58 t_omega_torsion 2.4 t_angle_deg 0.86 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.58 t_omega_torsion 2.4 t_angle_deg 0.86 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6525 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 117
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing