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Isopenicillin N synthase d-(L-a-aminoadipoyl)-(3R)-methyl-L-cysteine D-a-hydroxyisovaleryl ester complex (Oxygen exposed 5 minutes 20 bar)
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 (PH8.5), pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.23 44.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.513 α = 90 b = 70.789 β = 90 c = 100.813 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 ADSC CCD TOROIDAL MIRROR 2001-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.39 71 96.4 0.05 18.2 4.5 56205 18
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 1.46 1.54 92.6 0.31 4.2 3.6
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 1.46 57.74 53959 2208 95.9 0.17 0.169 0.1777 0.183 0.1952 RANDOM 15.36
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] 0.55 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.525 r_dihedral_angle_1_deg 5.251 r_scangle_it 3.679 r_scbond_it 2.388 r_angle_refined_deg 1.614 r_mcangle_it 1.581 r_angle_other_deg 1.07 r_mcbond_it 0.902 r_symmetry_vdw_refined 0.254 r_symmetry_vdw_other 0.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.525 r_dihedral_angle_1_deg 5.251 r_scangle_it 3.679 r_scbond_it 2.388 r_angle_refined_deg 1.614 r_mcangle_it 1.581 r_angle_other_deg 1.07 r_mcbond_it 0.902 r_symmetry_vdw_refined 0.254 r_symmetry_vdw_other 0.235 r_nbd_refined 0.226 r_nbd_other 0.19 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.095 r_nbtor_other 0.025 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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_refined 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 2607 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling