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Structure of Penicillin V acylase from Agrobacterium tumefaciens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.1M HEPES pH 7.5, 12% (w/v) PEG 3350, PEG Rx crystallization screen
Crystal Properties Matthews coefficient Solvent content 2.48 50.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.66 α = 90 b = 134.771 β = 90 c = 215.075 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M Rh coated collimating mirrors, K-B focusing mirrors 2014-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.988 SSRL BL12-2
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 2.8 39.55 99.9 0.136 11.9 7 37299
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 2.8 2.95 99.9 0.49 4 7
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 4WL2 2.8 38.067 35236 2000 99.79 0.21037 0.20843 0.2121 0.24505 0.2473 RANDOM 37.717
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] 0.12 -0.15 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.43 r_dihedral_angle_4_deg 17.247 r_dihedral_angle_3_deg 16.661 r_long_range_B_refined 8.093 r_long_range_B_other 8.093 r_dihedral_angle_1_deg 6.061 r_scangle_other 4.908 r_mcangle_it 4.276 r_mcangle_other 4.276 r_angle_other_deg 3.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.43 r_dihedral_angle_4_deg 17.247 r_dihedral_angle_3_deg 16.661 r_long_range_B_refined 8.093 r_long_range_B_other 8.093 r_dihedral_angle_1_deg 6.061 r_scangle_other 4.908 r_mcangle_it 4.276 r_mcangle_other 4.276 r_angle_other_deg 3.679 r_scbond_it 3.276 r_scbond_other 3.276 r_mcbond_it 2.627 r_mcbond_other 2.626 r_angle_refined_deg 1.599 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10180 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement