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Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PNK PDB ENTRY 1PNK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.41 48.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.2 α = 90 b = 131.7 β = 105.9 c = 64 γ = 90
Symmetry Space Group P 1 21 1
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 MAR300 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 1.3 20 95.5 0.075 20.5 3.6 190229 15.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.31 82 0.244 3.4
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PNK 1.8 30 74330 2297 96.5 0.153 0.1546 0.19 0.1909 RANDOM 16.9
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 p_transverse_tor 27.2 p_special_tor 15 p_staggered_tor 13.5 p_scangle_it 5.791 p_scbond_it 4.657 p_planar_tor 4.1 p_mcangle_it 2.84 p_mcbond_it 2.367 p_multtor_nbd 0.253 p_singtor_nbd 0.169
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 27.2 p_special_tor 15 p_staggered_tor 13.5 p_scangle_it 5.791 p_scbond_it 4.657 p_planar_tor 4.1 p_mcangle_it 2.84 p_mcbond_it 2.367 p_multtor_nbd 0.253 p_singtor_nbd 0.169 p_xyhbond_nbd 0.161 p_chiral_restr 0.143 p_planar_d 0.038 p_angle_d 0.034 p_plane_restr 0.0237 p_bond_d 0.017 p_angle_deg p_hb_or_metal_coord p_xhyhbond_nbd p_orthonormal_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6078 Nucleic Acid Atoms Solvent Atoms 701 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing