☰ Navigation Tabs
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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.27 42.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.3 α = 90 b = 131.6 β = 105.9 c = 63.9 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 MAR scanner 300 mm plate 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 11.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1PNK 1.3 20 181046 5653 95.5 0.148 0.169 0.1774 RANDOM 15.5
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_scangle_it 4.467 p_scbond_it 3.388 p_mcangle_it 1.982 p_mcbond_it 1.536 p_chiral_restr 0.128 p_planar_d 0.04 p_angle_d 0.031 p_plane_restr 0.026 p_bond_d 0.018 p_angle_deg
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 4.467 p_scbond_it 3.388 p_mcangle_it 1.982 p_mcbond_it 1.536 p_chiral_restr 0.128 p_planar_d 0.04 p_angle_d 0.031 p_plane_restr 0.026 p_bond_d 0.018 p_angle_deg p_hb_or_metal_coord p_singtor_nbd p_multtor_nbd p_xhyhbond_nbd p_xyhbond_nbd p_planar_tor p_staggered_tor p_orthonormal_tor p_transverse_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6086 Nucleic Acid Atoms Solvent Atoms 923 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing