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Altered substrate specificity mutant of penicillin acylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PNK PDB ENTRY 1PNK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.2 50MM MOPS PH 7.2, 12% MME PEG2K, STREAK-SEEDING
Crystal Properties Matthews coefficient Solvent content 2.4 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.02 α = 70.58 b = 64.23 β = 72.81 c = 70.67 γ = 73.84
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 IMAGE PLATE RIGAKU IMAGE PLATE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 20 93 0.04 14.8 2 50677
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 2.43 80 0.101 7.1 1.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PNK 2 19.8 48141 2536 100 0.152 0.1642 0.194 0.2033 RANDOM 16.47
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 0.46 0.09 -0.63 1.09 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.99 r_mcangle_it 1.8 r_scangle_it 1.788 r_angle_refined_deg 1.683 r_dihedral_angle_1_deg 1.368 r_nbtor_other 1.127 r_scbond_it 1.112 r_mcbond_it 1.091 r_angle_other_deg 0.854 r_nbd_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.99 r_mcangle_it 1.8 r_scangle_it 1.788 r_angle_refined_deg 1.683 r_dihedral_angle_1_deg 1.368 r_nbtor_other 1.127 r_scbond_it 1.112 r_mcbond_it 1.091 r_angle_other_deg 0.854 r_nbd_refined 0.326 r_symmetry_vdw_other 0.294 r_nbd_other 0.238 r_symmetry_vdw_refined 0.209 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.108 r_metal_ion_refined 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6061 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement DENZO data reduction Agrovata data scaling ROTAVATA data scaling AMoRE phasing