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X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with a 3,4- dichlorophenyl-substituted fosmidomycin analogue and manganese.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JD2 PDB ENTRY 2JD2
Crystallization Crystal Properties Matthews coefficient Solvent content 2.3 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.622 α = 90 b = 67.318 β = 107.38 c = 84.301 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 110 CCD MARRESEARCH SX-165 2008-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 MAX II I911-2
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 2.05 40 99.5 0.06 18.8 3.7 46664
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 2.05 2.16 99 0.43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2JD2 2.05 40 44300 2352 99.55 0.21194 0.20927 0.2089 0.26146 0.2546 RANDOM 35.305
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] -0.81 -0.92 0.91 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.479 r_dihedral_angle_4_deg 16.273 r_dihedral_angle_3_deg 14.423 r_dihedral_angle_1_deg 4.871 r_scangle_it 2.127 r_scbond_it 1.284 r_angle_refined_deg 1.05 r_mcangle_it 0.911 r_mcbond_it 0.513 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.479 r_dihedral_angle_4_deg 16.273 r_dihedral_angle_3_deg 14.423 r_dihedral_angle_1_deg 4.871 r_scangle_it 2.127 r_scbond_it 1.284 r_angle_refined_deg 1.05 r_mcangle_it 0.911 r_mcbond_it 0.513 r_nbtor_refined 0.294 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.153 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5413 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing