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Penicillin Acylase with Phenyl Proprionic Acid
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 VAPOR DIFFUSION, HANGING DROP 7.2 277 MOPS BUFFER, PEG MME 2K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.12 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.331 α = 72.54 b = 64.551 β = 73.29 c = 64.347 γ = 73.58
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 MACSCIENCE mirrors 2000-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.15 30 95.3 0.068 10.1 1.74 40070 38187 -3 34.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 87.5 0.229 2.7
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PNK 2.15 30.15 36555 1632 91.2 0.18376 0.18215 0.21646 RANDOM 22.081
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] -0.47 -0.3 0.05 -0.04 -0.04 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.201 r_dihedral_angle_1_deg 4.07 r_scangle_it 3.429 r_scbond_it 2.15 r_angle_refined_deg 1.589 r_mcangle_it 1.347 r_angle_other_deg 0.88 r_mcbond_it 0.75 r_symmetry_vdw_refined 0.454 r_symmetry_hbond_refined 0.371
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.201 r_dihedral_angle_1_deg 4.07 r_scangle_it 3.429 r_scbond_it 2.15 r_angle_refined_deg 1.589 r_mcangle_it 1.347 r_angle_other_deg 0.88 r_mcbond_it 0.75 r_symmetry_vdw_refined 0.454 r_symmetry_hbond_refined 0.371 r_nbd_refined 0.238 r_nbd_other 0.214 r_symmetry_vdw_other 0.214 r_xyhbond_nbd_refined 0.168 r_nbtor_other 0.124 r_metal_ion_refined 0.098 r_chiral_restr 0.097 r_xyhbond_nbd_other 0.02 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6072 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling TRUNCATE data reduction CNS refinement DENZO data reduction CCP4 data scaling CNS phasing