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CPR-C4 - novel protease from the Candidate Phyla Radiation (CPR)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OB6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 sodium malonate dibasic monohydrate
Crystal Properties Matthews coefficient Solvent content 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.307 α = 90 b = 79.731 β = 90 c = 126.196 γ = 90
Symmetry Space Group I 2 2 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 6M 2019-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.2819 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.581 67.405 98.9 0.505 0.562 0.243 0.968 6.8 9.7 9190
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.581 2.69 7.895 8.889 3.982 0.181 8.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7OB6 2.682 67.405 8193 398 98.747 0.236 0.2348 0.2506 0.2365 49.032
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] -1.94 6.08 -4.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.876 r_dihedral_angle_4_deg 19.829 r_lrange_it 14.438 r_dihedral_angle_3_deg 14.335 r_scangle_it 8.816 r_dihedral_angle_1_deg 7.331 r_mcangle_it 5.989 r_scbond_it 5.74 r_mcbond_it 3.833 r_angle_refined_deg 1.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.876 r_dihedral_angle_4_deg 19.829 r_lrange_it 14.438 r_dihedral_angle_3_deg 14.335 r_scangle_it 8.816 r_dihedral_angle_1_deg 7.331 r_mcangle_it 5.989 r_scbond_it 5.74 r_mcbond_it 3.833 r_angle_refined_deg 1.406 r_symmetry_nbd_refined 0.304 r_nbtor_refined 0.296 r_ext_dist_refined_d 0.223 r_nbd_refined 0.195 r_symmetry_xyhbond_nbd_refined 0.194 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.093 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1653 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling DIALS data reduction pointless data scaling PHASER phasing