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Crystal structure of the Brucella abortus enzyme catalyzing the first committed step of the methylerythritol 4-phosphate pathway.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UPL pdb entry 3UPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 14-20% PEG4000, 0.1M HEPES, 0.2M magnesium chloride, 0.5 mM fosmidomycin , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.391 α = 68.79 b = 63.379 β = 75.54 c = 79.334 γ = 72.07
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 MARMOSAIC 225 mm CCD mirrors 2010-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 1.8 40 93.5 0.038 18.9 1.9 78348 73258 -3
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 1.8 1.86 77.6 0.25 2.73 1.6 6096
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 (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 MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3UPL 1.8 39.55 73258 69601 3657 93.45 0.1648 0.1648 0.1627 0.1813 0.2042 0.2176 RANDOM 18.47
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] 0.86 -0.23 -0.37 -0.32 0.57 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.97 r_dihedral_angle_4_deg 19.482 r_dihedral_angle_3_deg 13.69 r_dihedral_angle_1_deg 6.145 r_scangle_it 4.802 r_scbond_it 2.964 r_angle_refined_deg 1.835 r_mcangle_it 1.688 r_angle_other_deg 1.068 r_mcbond_it 1.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.97 r_dihedral_angle_4_deg 19.482 r_dihedral_angle_3_deg 13.69 r_dihedral_angle_1_deg 6.145 r_scangle_it 4.802 r_scbond_it 2.964 r_angle_refined_deg 1.835 r_mcangle_it 1.688 r_angle_other_deg 1.068 r_mcbond_it 1.002 r_mcbond_other 0.336 r_chiral_restr 0.116 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6502 Nucleic Acid Atoms Solvent Atoms 655 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DNA data collection MOLREP phasing