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X-ray structure of Clostridium perfringens autolysin catalytic domain in the P1 form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 10% (w/v) PEG 3000, 100mM CHES/ sodium hydroxide
Crystal Properties Matthews coefficient Solvent content 1.84 33.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.13 α = 94.79 b = 47.52 β = 89.916 c = 64.31 γ = 96.29
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS VII 2016-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.6 36.53 98.9 0.995 7.5 5.6 56867
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 1.6 1.64 0.809
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 1.6 36.503 56867 2811 98.904 0.165 0.1629 0.1739 0.1968 0.2044 19.429
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] 0.016 0.001 0.004 -0.04 0.012 0.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.688 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 14.114 r_dihedral_angle_1_deg 6.192 r_lrange_it 5.389 r_lrange_other 5.262 r_scangle_other 3.561 r_scangle_it 3.56 r_mcangle_other 2.859 r_mcangle_it 2.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.688 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 14.114 r_dihedral_angle_1_deg 6.192 r_lrange_it 5.389 r_lrange_other 5.262 r_scangle_other 3.561 r_scangle_it 3.56 r_mcangle_other 2.859 r_mcangle_it 2.856 r_scbond_it 2.326 r_scbond_other 2.323 r_mcbond_it 1.898 r_mcbond_other 1.88 r_angle_refined_deg 1.634 r_angle_other_deg 1.476 r_nbd_refined 0.217 r_nbd_other 0.207 r_symmetry_nbd_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.185 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_other 0.089 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4076 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing