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Crystal Structure of Open form of Menaquinone-Specific Isochorismate Synthase, MenF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop vapor diffusion 8 298 well solution: 0.2M sodium citrate, 6% glycerol, 8% PEG 3350, 5mM chorismic acid. protein solution: 50mM Tris, 5 mM magnesium chloride, 1 mM DTT, pH 7.6, 20 mg/mL. Drops were equal volumes well and protein., sitting drop vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.54 51.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.37 α = 90 b = 72.37 β = 90 c = 164.01 γ = 120
Symmetry Space Group P 32 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 105 IMAGE PLATE RIGAKU RAXIS IV++ 2007-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.95 19.67 98.1 0.064 14.7 7.97 36355
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) 1.95 2.02 84.8 0.474 2.6 4.61 3084
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.95 19.67 35738 1804 96.43 0.248 0.245 0.254 0.308 0.3131 RANDOM 48.543
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] 1.09 0.54 1.09 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.792 r_dihedral_angle_3_deg 20.588 r_dihedral_angle_4_deg 15.875 r_dihedral_angle_1_deg 7.575 r_scangle_it 3.785 r_scbond_it 2.679 r_angle_refined_deg 1.975 r_mcangle_it 1.794 r_mcbond_it 1.108 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.792 r_dihedral_angle_3_deg 20.588 r_dihedral_angle_4_deg 15.875 r_dihedral_angle_1_deg 7.575 r_scangle_it 3.785 r_scbond_it 2.679 r_angle_refined_deg 1.975 r_mcangle_it 1.794 r_mcbond_it 1.108 r_nbtor_refined 0.311 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.222 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.149 r_symmetry_hbond_refined 0.133 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3432 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 13
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction