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Crystal structure of a variant of penicillin G acylase from Bacillaceae i. s. sp. FJAT-27231 with reduced surface entropy and additionally engineered crystal contact.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 293 100 mM HEPES pH 7.5
30 mg/ml PEG 8000
Microbatch under paraffin oil
Cryoprotection: 10 % (v/v) 2,3-(R,R)-butanediol
Crystal Properties Matthews coefficient Solvent content 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.322 α = 90 b = 101.627 β = 90 c = 139.435 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 EIGER X 16M 2021-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 1.2 82.13 96.3 0.054 0.056 0.016 0.999 21.9 11.6 261459
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 1.2 1.26 79.1 0.536 0.583 0.221 0.874 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6NVX 1.2 46.04 1.36 261330 13202 96.25 0.1448 0.1442 0.1442 0.1559 0.1559
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.162 f_angle_d 0.995 f_chiral_restr 0.079 f_plane_restr 0.012 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5807 Nucleic Acid Atoms Solvent Atoms 842 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement autoPROC data processing Aimless data scaling XDS data reduction PHASER phasing