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CHAP domain of Pneumococcal Endopeptidase PcsB - Active Site Mutant C292A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 100mM BICINE (pH 9), 10% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.36 47.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.878 α = 90 b = 47.92 β = 97.93 c = 84.424 γ = 90
Symmetry Space Group P 1 2 1
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 EIGER X 9M 2023-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95371 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 1.68 49.66 99.5 0.169 0.186 0.078 0.993 5.8 5.5 62042
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 1.68 1.71 1.454 1.045 0.849 0.435 3.7
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 1.8 49.66 48351 2644 99.97 0.2167 0.21529 0.2219 0.24215 0.2428 RANDOM 18.029
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] -0.1 -0.01 0.03 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.978 r_dihedral_angle_1_deg 6.476 r_dihedral_angle_2_deg 5.866 r_long_range_B_refined 4.195 r_long_range_B_other 4.104 r_scangle_other 2.759 r_mcangle_it 2.26 r_mcangle_other 2.26 r_scbond_it 1.857 r_scbond_other 1.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.978 r_dihedral_angle_1_deg 6.476 r_dihedral_angle_2_deg 5.866 r_long_range_B_refined 4.195 r_long_range_B_other 4.104 r_scangle_other 2.759 r_mcangle_it 2.26 r_mcangle_other 2.26 r_scbond_it 1.857 r_scbond_other 1.856 r_mcbond_it 1.563 r_mcbond_other 1.561 r_angle_refined_deg 1.458 r_angle_other_deg 0.533 r_chiral_restr 0.072 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 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 3294 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction