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X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with 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 = 69.826 α = 90 b = 67.477 β = 107.48 c = 84.621 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 ADSC CCD 2008-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.9 40 98.5 0.07 16.2 3.6 58370
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 1.9 2 97.8 0.45
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 1.9 40 55426 2943 98.49 0.19762 0.19522 0.1936 0.2422 0.2402 RANDOM 29.4
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] -0.78 -0.9 -0.07 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.23 r_dihedral_angle_4_deg 18.622 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 5.327 r_scangle_it 2.58 r_scbond_it 1.59 r_angle_refined_deg 1.124 r_mcangle_it 1.098 r_mcbond_it 0.639 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.23 r_dihedral_angle_4_deg 18.622 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 5.327 r_scangle_it 2.58 r_scbond_it 1.59 r_angle_refined_deg 1.124 r_mcangle_it 1.098 r_mcbond_it 0.639 r_nbtor_refined 0.297 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 5505 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing