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Structure and Mechanism of MenF, the Menaquinone-Specific Isochorismate Synthase from Escherichia Coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.8 M potassium sodium tartrate, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.44 64.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.408 α = 90 b = 146.408 β = 90 c = 125.6 γ = 90
Symmetry Space Group P 43 21 2
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 2004-07-24 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 4 2004-10-31 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.25360 NSLS X26C 2 SYNCHROTRON NSLS BEAMLINE X26C 0.9745, 0.97971 NSLS X26C
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 2.5 50 99.1 0.099 47401 2 2
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) 2.5 2.54 85.4 85.4 0.543
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 2.5 25 47073 44680 2393 98.65 0.232 0.232 0.229 0.2623 0.276 0.3015 RANDOM 57.033
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] -0.05 -0.05 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.302 r_dihedral_angle_3_deg 20.43 r_dihedral_angle_4_deg 16.579 r_dihedral_angle_1_deg 8.959 r_scangle_it 2.206 r_angle_refined_deg 1.592 r_scbond_it 1.401 r_mcangle_it 0.93 r_mcbond_it 0.541 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.302 r_dihedral_angle_3_deg 20.43 r_dihedral_angle_4_deg 16.579 r_dihedral_angle_1_deg 8.959 r_scangle_it 2.206 r_angle_refined_deg 1.592 r_scbond_it 1.401 r_mcangle_it 0.93 r_mcbond_it 0.541 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.26 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.221 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6693 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction