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Isopenicillin N synthase with substrate analogue L,L,L-ACOMP (unexposed)
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 2.07 40.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.537 α = 90 b = 71.314 β = 90 c = 100.651 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 MARRESEARCH MIRRORS 2005-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 1.99 18.17 97.7 0.09 19.5 6.6 23160 17.57
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 1.99 2.1 85.9 0.27 7.4 6.1
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 2 58.22 22198 909 99 0.169 0.167 0.1734 0.216 0.2223 RANDOM 11.76
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] -0.35 0.63 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.496 r_dihedral_angle_3_deg 13.755 r_dihedral_angle_4_deg 8.975 r_dihedral_angle_1_deg 6.752 r_scangle_it 4.281 r_scbond_it 3.095 r_angle_refined_deg 1.798 r_mcangle_it 1.728 r_mcbond_it 1.41 r_angle_other_deg 1.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.496 r_dihedral_angle_3_deg 13.755 r_dihedral_angle_4_deg 8.975 r_dihedral_angle_1_deg 6.752 r_scangle_it 4.281 r_scbond_it 3.095 r_angle_refined_deg 1.798 r_mcangle_it 1.728 r_mcbond_it 1.41 r_angle_other_deg 1.097 r_symmetry_vdw_other 0.253 r_nbd_refined 0.219 r_nbd_other 0.195 r_nbtor_refined 0.184 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.116 r_symmetry_hbond_refined 0.112 r_nbtor_other 0.09 r_bond_refined_d 0.024 r_bond_other_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.001 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 2645 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing