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Isopenicillin N synthase with substrate analogue 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 1.99 37.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.697 α = 90 b = 71.161 β = 90 c = 100.912 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 2005-04-17 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 1.8 34.3 98.4 0.1 21 9 31926 13.47
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 1.79 1.89 89 0.27 7.2 8.5
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 1.8 30.41 30604 1245 99.8 0.152 0.151 0.1575 0.19 0.194 RANDOM 5.5
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] 0.04 0.03 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.828 r_dihedral_angle_3_deg 12.53 r_dihedral_angle_4_deg 9.133 r_dihedral_angle_1_deg 6.422 r_scangle_it 3.861 r_scbond_it 2.785 r_angle_other_deg 2.235 r_angle_refined_deg 1.722 r_mcangle_it 1.446 r_mcbond_it 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.828 r_dihedral_angle_3_deg 12.53 r_dihedral_angle_4_deg 9.133 r_dihedral_angle_1_deg 6.422 r_scangle_it 3.861 r_scbond_it 2.785 r_angle_other_deg 2.235 r_angle_refined_deg 1.722 r_mcangle_it 1.446 r_mcbond_it 1.24 r_symmetry_vdw_other 0.288 r_nbd_other 0.221 r_nbd_refined 0.218 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.184 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.114 r_nbtor_other 0.086 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 r_bond_other_d 0.002 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 345 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing