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Structure of penicillin V acylase from Pectobacterium atrosepticum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 14% PEG 3350, 0.2 M sodium potassium tartrate, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.63 53.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.447 α = 90 b = 150.206 β = 90 c = 185.63 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 CCD RAYONIX MX-225 2014-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 1.435 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 65.7 88.5 0.117 0.117 11.7 7.26 101210 488
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 2.5 2.64 58.2 0.786 1.8 4.99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 63.43 96055 5077 88.03 0.21981 0.2183 0.2209 0.24839 0.249 RANDOM 42.294
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] 0.37 -0.64 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.871 r_dihedral_angle_4_deg 21.796 r_dihedral_angle_3_deg 20.286 r_long_range_B_other 9.004 r_long_range_B_refined 9.003 r_dihedral_angle_1_deg 6.812 r_mcangle_it 5.912 r_mcangle_other 5.911 r_scangle_other 5.523 r_mcbond_it 3.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.871 r_dihedral_angle_4_deg 21.796 r_dihedral_angle_3_deg 20.286 r_long_range_B_other 9.004 r_long_range_B_refined 9.003 r_dihedral_angle_1_deg 6.812 r_mcangle_it 5.912 r_mcangle_other 5.911 r_scangle_other 5.523 r_mcbond_it 3.662 r_mcbond_other 3.661 r_scbond_it 3.445 r_scbond_other 3.445 r_angle_refined_deg 1.721 r_angle_other_deg 1.555 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.007 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 21688 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing MOSFLM data processing