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Isopenicillin N synthase with AC-D-methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BK0 PDB ENTRY 1BK0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 1.0M LITHIUM SULPHATE, 76MM TRIS/HCL, PH 8.5, 2.0MM FERROUS SULPHATE, 2.6MG/ML TRIPEPTIDE, 25MG/ML IPNS
Crystal Properties Matthews coefficient Solvent content 2.23 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.523 α = 90 b = 70.882 β = 90 c = 100.923 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 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 1998-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 1.4 20.33 83.8 0.08 9.4 2.5 55964 11
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 1.4 1.48 85.1 0.43 1.9 2.4
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 PDB ENTRY 1BK0 1.4 19.45 53070 2213 83.16 0.14701 0.14489 0.1434 0.19934 0.1978 RANDOM 14.727
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] 0.41 -0.02 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.011 r_dihedral_angle_4_deg 14.961 r_dihedral_angle_3_deg 12.216 r_scangle_it 7.445 r_dihedral_angle_1_deg 6.288 r_scbond_it 5.439 r_mcangle_it 3.7 r_rigid_bond_restr 2.875 r_mcbond_it 2.602 r_angle_refined_deg 2.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.011 r_dihedral_angle_4_deg 14.961 r_dihedral_angle_3_deg 12.216 r_scangle_it 7.445 r_dihedral_angle_1_deg 6.288 r_scbond_it 5.439 r_mcangle_it 3.7 r_rigid_bond_restr 2.875 r_mcbond_it 2.602 r_angle_refined_deg 2.068 r_chiral_restr 0.146 r_bond_refined_d 0.024 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2639 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling REFMAC phasing