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Crystal Structure of Mycobacterium tuberculosis MenB, a Key Enzyme in Vitamin K2 Biosynthesis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 dioxane, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.13 42.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.375 α = 90 b = 139.432 β = 97.29 c = 142.027 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 4 2002-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.1 NSLS X26C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 312176
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 50 312176 15654 97.43 0.19749 0.19749 0.19538 0.21861 RANDOM 33.313
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] -0.1 0.06 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.943 r_scangle_it 4.804 r_scbond_it 3.098 r_mcangle_it 1.981 r_angle_refined_deg 1.794 r_mcbond_it 1.194 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.186 r_symmetry_vdw_refined 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.943 r_scangle_it 4.804 r_scbond_it 3.098 r_mcangle_it 1.981 r_angle_refined_deg 1.794 r_mcbond_it 1.194 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.186 r_symmetry_vdw_refined 0.16 r_chiral_restr 0.135 r_bond_refined_d 0.023 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25503 Nucleic Acid Atoms Solvent Atoms 2984 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling BEAST phasing COMO phasing