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Structure of truncated mutant CYS1GLY of penicillin V acylase from bacillus sphaericus co-crystallized with penicillin V
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 pH 6.4, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.14 60.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.73 α = 90 b = 158.89 β = 90 c = 90.742 γ = 90
Symmetry Space Group C 2 2 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 2003-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 20 89.6 78639 28157
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PVA 2.6 20 24808 1320 89.7 0.24045 0.23881 0.2703 RANDOM 46.447
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] -2.58 -9.21 11.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.591 r_scangle_it 5.547 r_scbond_it 4.019 r_mcangle_it 2.682 r_mcbond_it 1.717 r_angle_refined_deg 0.979 r_nbd_refined 0.286 r_symmetry_vdw_refined 0.231 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.591 r_scangle_it 5.547 r_scbond_it 4.019 r_mcangle_it 2.682 r_mcbond_it 1.717 r_angle_refined_deg 0.979 r_nbd_refined 0.286 r_symmetry_vdw_refined 0.231 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.178 r_symmetry_hbond_refined 0.134 r_bond_refined_d 0.054 r_gen_planes_refined 0.019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5161 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing