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Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with ThDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 12% PEG 8K, 10% glycerol, 1mM ThDP, 5mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.46 49.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.353 α = 75.99 b = 90.463 β = 83 c = 169.17 γ = 64.15
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 270 mirrors 2009-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6C1 1.0000 PAL/PLS 6C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 50 83.5 0.15 0.26 6.22 2.4 141599 114098 14.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 48.1 0.15 0.26 1.8 1.5 4413
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2JLC 2.6 47.69 141599 114098 5978 83.51 0.19946 0.19667 0.2009 0.25271 0.2226 RANDOM 14.503
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] -0.09 0.04 -0.02 -0.02 -0.01 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.259 r_dihedral_angle_4_deg 20.994 r_dihedral_angle_3_deg 19.38 r_dihedral_angle_1_deg 6.895 r_scangle_it 3.055 r_scbond_it 1.868 r_angle_refined_deg 1.764 r_mcangle_it 1.108 r_mcbond_it 0.59 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.259 r_dihedral_angle_4_deg 20.994 r_dihedral_angle_3_deg 19.38 r_dihedral_angle_1_deg 6.895 r_scangle_it 3.055 r_scbond_it 1.868 r_angle_refined_deg 1.764 r_mcangle_it 1.108 r_mcbond_it 0.59 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 34608 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 243
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling