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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 6.5 298 well solution: 0.1M Bis-Tris pH 6.5, 20% PEG-MME 5000. protein solution: 50mM Tris pH 7.8, 50 mM magnesium sulfate. Drops were equal volumes well and protein., sitting drop vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.13 42.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.28 α = 90 b = 70.49 β = 90 c = 90.28 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 105 IMAGE PLATE RIGAKU RAXIS IV++ 2004-01-01 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 1.99 29.62 99.2 0.074 9.2 2.97 28882
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) 1.99 2.07 95.7 0.322 3.2 2.82 2745
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 2 20 28501 1457 99.06 0.206 0.202 0.2045 0.284 0.2867 RANDOM 28.943
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] -1.57 -0.65 2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.979 r_dihedral_angle_4_deg 22.582 r_dihedral_angle_3_deg 20.863 r_dihedral_angle_1_deg 7.444 r_scangle_it 4.242 r_scbond_it 2.975 r_angle_refined_deg 2.023 r_mcangle_it 1.746 r_mcbond_it 1.091 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.979 r_dihedral_angle_4_deg 22.582 r_dihedral_angle_3_deg 20.863 r_dihedral_angle_1_deg 7.444 r_scangle_it 4.242 r_scbond_it 2.975 r_angle_refined_deg 2.023 r_mcangle_it 1.746 r_mcbond_it 1.091 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.297 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.154 r_bond_refined_d 0.021 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3482 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 16
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction