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Crystal structure of Peptiligase mutant - L217H/M222P/A225N/F189W
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AM5 D_1292111626
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 1.2 -1.8 M ammonium tartrate
Crystal Properties Matthews coefficient Solvent content 3.18 61.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.44 α = 90 b = 105.44 β = 90 c = 192.08 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 2019-12-17 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 2.7 64.03 96.8 0.282 0.309 0.122 0.969 6.1 5.5 29451
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 2.7 2.83 93.9 1.137 1.247 0.494 0.369 5.4
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_1292111626 2.7 58.96 27937 1458 96.22 0.2143 0.2122 0.2173 0.2523 0.2564 RANDOM 39.967
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] -0.14 -0.14 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.774 r_dihedral_angle_4_deg 21.31 r_dihedral_angle_3_deg 16.96 r_dihedral_angle_1_deg 6.724 r_angle_refined_deg 1.686 r_angle_other_deg 1.326 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.774 r_dihedral_angle_4_deg 21.31 r_dihedral_angle_3_deg 16.96 r_dihedral_angle_1_deg 6.724 r_angle_refined_deg 1.686 r_angle_other_deg 1.326 r_chiral_restr 0.072 r_bond_refined_d 0.01 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 5728 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing