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Crystal structure of Peptiligase mutant - M222P/L217H/A225N/F189W/N218D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AM3 D_1292111488
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 1.2 M Ammonium sulfate, 0.25 PEG3350, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 3 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.798 α = 90 b = 105.798 β = 90 c = 191.516 γ = 90
Symmetry Space Group P 41 2 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 2018-11-12 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 2.61 48.61 99.8 0.263 0.281 0.099 0.99 8.3 8 33957
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 2.61 2.72 98.8 0.994 1.066 0.381 0.583 7.5
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 D_1292111488 2.61 48.59 32234 1661 99.78 0.1975 0.1955 0.2029 0.2373 0.2414 RANDOM 40.479
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] 1.17 1.17 -2.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.845 r_dihedral_angle_3_deg 15.73 r_dihedral_angle_4_deg 11.96 r_dihedral_angle_1_deg 6.798 r_angle_refined_deg 1.559 r_angle_other_deg 1.326 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.845 r_dihedral_angle_3_deg 15.73 r_dihedral_angle_4_deg 11.96 r_dihedral_angle_1_deg 6.798 r_angle_refined_deg 1.559 r_angle_other_deg 1.326 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5702 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing