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Crystal structure of Peptiligase mutant - M222P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 1.4 M MgSO4 , 0.1 M MES pH 6.5.
Crystal Properties Matthews coefficient Solvent content 1.8 37.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.489 α = 90 b = 58.489 β = 90 c = 126.005 γ = 90
Symmetry Space Group P 41 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 IMAGE PLATE MARRESEARCH 2019-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.5418
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 1.61 42.86 99.6 0.05 0.054 0.019 0.999 26 7.6 29222
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 1.61 1.64 91.6 0.197 0.214 0.081 0.982 6.6
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 5OX2 1.61 42.86 27701 1443 99.61 0.1352 0.134 0.1343 0.1591 0.1605 RANDOM 13.749
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] 0.02 0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.767 r_dihedral_angle_4_deg 13.827 r_dihedral_angle_3_deg 12.259 r_dihedral_angle_1_deg 5.869 r_angle_other_deg 1.605 r_angle_refined_deg 1.585 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.767 r_dihedral_angle_4_deg 13.827 r_dihedral_angle_3_deg 12.259 r_dihedral_angle_1_deg 5.869 r_angle_other_deg 1.605 r_angle_refined_deg 1.585 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1898 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 34
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing