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CHAP domain of Pneumococcal Endopeptidase PcsB
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 Sodium citrate(pH 5.6), 500mM NaCl, 4 % v/v Polyethyleneimine
Crystal Properties Matthews coefficient Solvent content 2.01 38.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.28 α = 90 b = 117.38 β = 90 c = 47.69 γ = 90
Symmetry Space Group P 21 21 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 EIGER2 XE 9M 2022-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.7 45 100 0.83 19.5 13.3 52851
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 0.252
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 44.222 52851 2634 99.966 0.173 0.1719 0.1833 0.1941 0.1994 18.687
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] 0.002 -0.003 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.626 r_dihedral_angle_4_deg 12.94 r_dihedral_angle_3_deg 11.697 r_dihedral_angle_1_deg 6.482 r_lrange_it 4.48 r_lrange_other 4.448 r_scangle_it 3.692 r_scangle_other 3.691 r_scbond_it 2.637 r_scbond_other 2.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.626 r_dihedral_angle_4_deg 12.94 r_dihedral_angle_3_deg 11.697 r_dihedral_angle_1_deg 6.482 r_lrange_it 4.48 r_lrange_other 4.448 r_scangle_it 3.692 r_scangle_other 3.691 r_scbond_it 2.637 r_scbond_other 2.636 r_mcangle_it 2.426 r_mcangle_other 2.426 r_angle_refined_deg 1.745 r_mcbond_it 1.728 r_mcbond_other 1.712 r_angle_other_deg 1.622 r_nbd_other 0.255 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.2 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.147 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3282 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement Aimless data scaling REFMAC phasing