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Crystal Structure of Penicillin V acylase from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PVA PDB ENTRY 2PVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 291 4M sodium formate in 100mM Tris-HCl buffer, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.23 61.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.963 α = 90 b = 307.956 β = 90 c = 56.003 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 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2002-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.497 20 31859 40.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.497 2.562 96.24
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PVA 2.5 20 31859 1705 98.65 0.15785 0.15466 0.1554 0.2179 RANDOM 40.756
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] 0.01 -3.35 3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.708 r_dihedral_angle_4_deg 22.909 r_dihedral_angle_3_deg 19.579 r_dihedral_angle_1_deg 7.424 r_scangle_it 6.476 r_scbond_it 4.238 r_mcangle_it 2.604 r_angle_refined_deg 2.341 r_mcbond_it 1.627 r_symmetry_hbond_refined 0.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.708 r_dihedral_angle_4_deg 22.909 r_dihedral_angle_3_deg 19.579 r_dihedral_angle_1_deg 7.424 r_scangle_it 6.476 r_scbond_it 4.238 r_mcangle_it 2.604 r_angle_refined_deg 2.341 r_mcbond_it 1.627 r_symmetry_hbond_refined 0.396 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.296 r_nbd_refined 0.263 r_xyhbond_nbd_refined 0.227 r_chiral_restr 0.182 r_bond_refined_d 0.03 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5082 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing