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The ternary complex of PrnB (the second enzyme in pyrrolnitrin biosynthesis pathway), 7-Cl-L-tryptophan and cyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V7J PDB ENTRY 2V7J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.4 0.1M BIS-TRIS BUFFER PH 6.4, 10% PEG3350, 0.2M MGSO4
Crystal Properties Matthews coefficient Solvent content 2.9 58.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.427 α = 90 b = 79.525 β = 103.3 c = 92.303 γ = 90
Symmetry Space Group C 1 2 1
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 RIGAKU CCD OSMIC MIRRORS 2008-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2.13 24 97.5 0.08 20 3.6 24910 2 26.1
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 2.13 2.17 94.9 0.28 4.5 3.4
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 2V7J 2.13 24.22 24910 1375 97.43 0.16661 0.16485 0.1749 0.19895 0.2098 RANDOM 15.153
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] 0.23 0.35 -1.02 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.337 r_dihedral_angle_4_deg 21.346 r_dihedral_angle_3_deg 13.598 r_dihedral_angle_1_deg 5.026 r_scangle_it 3.345 r_scbond_it 2.032 r_angle_refined_deg 1.283 r_mcangle_it 1.15 r_mcbond_it 0.621 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.337 r_dihedral_angle_4_deg 21.346 r_dihedral_angle_3_deg 13.598 r_dihedral_angle_1_deg 5.026 r_scangle_it 3.345 r_scbond_it 2.032 r_angle_refined_deg 1.283 r_mcangle_it 1.15 r_mcbond_it 0.621 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2737 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling