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The C146A variant of an amidase from Pyrococcus horikoshii with bound acetamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YPA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 The crystallization condition is: 5mg/mL protein, 0.1M potassium chloride, 0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.1M acetamide; Imidazole; MES monohydrate (acid); 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.979 α = 68.09 b = 57.012 β = 85.16 c = 61.358 γ = 76.93
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 170 PIXEL DECTRIS EIGER2 XE 16M 2019-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.65 43.86 81.14 0.056 0.065 0.035 0.996 11.32 3.4 53852 22.57
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 1.65 1.709 30.28 0.3671 0.4444 0.2463 0.927 2.39 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 6YPA 1.65 43.85 51146 2661 81.14 0.1527 0.15115 0.163 0.18204 0.1922 RANDOM 29.106
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 0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.411 r_dihedral_angle_4_deg 16.634 r_dihedral_angle_3_deg 12.49 r_long_range_B_other 9.879 r_long_range_B_refined 9.862 r_scangle_other 9.208 r_scbond_it 6.61 r_scbond_other 6.608 r_dihedral_angle_1_deg 6.506 r_mcangle_other 4.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.411 r_dihedral_angle_4_deg 16.634 r_dihedral_angle_3_deg 12.49 r_long_range_B_other 9.879 r_long_range_B_refined 9.862 r_scangle_other 9.208 r_scbond_it 6.61 r_scbond_other 6.608 r_dihedral_angle_1_deg 6.506 r_mcangle_other 4.142 r_mcangle_it 4.13 r_mcbond_it 3.222 r_mcbond_other 3.207 r_angle_refined_deg 1.626 r_angle_other_deg 1.188 r_chiral_restr 0.11 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4224 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing