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N-acetylmuramoyl-L-alanine amidase LysC from Clostridium intestinale URNW
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SU5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.4 293 NaKHPO4, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.4 α = 90 b = 53.78 β = 90 c = 76.71 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 PILATUS3 S 6M 2018-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.21 14.9 99.8 0.07 1 12.1 5.3 47839
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.21 1.23 1.11 0.5 1.3
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 (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 6SU5 1.21 14.9 45430 2353 99.61 0.1225 0.1205 0.1228 0.1607 0.1239 RANDOM 16.156
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] -0.95 0.07 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.799 r_dihedral_angle_4_deg 19.262 r_dihedral_angle_3_deg 11.886 r_dihedral_angle_1_deg 6.604 r_rigid_bond_restr 4.233 r_angle_refined_deg 2.222 r_angle_other_deg 1.551 r_chiral_restr 0.13 r_bond_refined_d 0.018 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.799 r_dihedral_angle_4_deg 19.262 r_dihedral_angle_3_deg 11.886 r_dihedral_angle_1_deg 6.604 r_rigid_bond_restr 4.233 r_angle_refined_deg 2.222 r_angle_other_deg 1.551 r_chiral_restr 0.13 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1213 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction PDB_EXTRACT data extraction xia2 data scaling MOLREP phasing