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Crystal form 3 of CPR-C4: a cysteine protease from the Candidate Phyla Radiation
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 300 Lithium sulfate, Tris, PEG4000
Crystal Properties Matthews coefficient Solvent content 2.57 52.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.78 α = 90 b = 77.545 β = 90 c = 161.722 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 XE 16M 2021-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 2.248 44.302 98.1 0.085 0.092 0.035 0.999 17.1 12.4 27119
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 2.25 2.32 1.77 1.998 0.905 0.36 8.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7OB6 2.248 44.26 27063 1323 97.866 0.181 0.1788 0.1764 0.2246 0.2248 57.088
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] -0.058 0.085 -0.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.929 r_dihedral_angle_4_deg 15.341 r_dihedral_angle_3_deg 14.927 r_lrange_other 9.48 r_lrange_it 9.462 r_scangle_it 8.1 r_scangle_other 8.062 r_dihedral_angle_1_deg 7.428 r_mcangle_it 6.122 r_mcangle_other 6.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.929 r_dihedral_angle_4_deg 15.341 r_dihedral_angle_3_deg 14.927 r_lrange_other 9.48 r_lrange_it 9.462 r_scangle_it 8.1 r_scangle_other 8.062 r_dihedral_angle_1_deg 7.428 r_mcangle_it 6.122 r_mcangle_other 6.121 r_scbond_it 5.575 r_scbond_other 5.462 r_mcbond_it 4.543 r_mcbond_other 4.541 r_angle_refined_deg 1.442 r_angle_other_deg 1.226 r_xyhbond_nbd_refined 0.228 r_nbd_refined 0.201 r_symmetry_nbd_refined 0.185 r_symmetry_nbd_other 0.17 r_nbd_other 0.17 r_nbtor_refined 0.162 r_ncsr_local_group_1 0.08 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3493 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing Coot model building