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Crystal structure of an engineered variant of single-chain Penicillin G Acylase from Kluyvera cryocrescens (A1-Ac Rd3CHis)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 2M Ammonium sulfate, 100mM Bis-Tris
Crystal Properties Matthews coefficient Solvent content 3.9 68.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.7 α = 90 b = 102.7 β = 90 c = 255.01 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS 6M 2016-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.192 50 100 0.15 19 13 70875
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.192 2.28 0.399
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 4PEM 2.192 47.91 70766 1396 99.8 0.2254 0.2248 0.2133 0.2519 0.2311 RANDOM 46.01
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] -0.4151 -0.4151 0.8302
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.57 t_omega_torsion 3.17 t_angle_deg 0.91 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.57 t_omega_torsion 3.17 t_angle_deg 0.91 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6022 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 11
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing