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X-ray structure of mutant 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C82 PDB ENTRY 2C82
Crystallization Crystal Properties Matthews coefficient Solvent content 2.2 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.629 α = 90 b = 65.611 β = 102.02 c = 86.016 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 2006-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.3 35 100 0.1 13.4 4.5 32964
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 2.3 2.36 100 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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2C82 2.3 35 31255 1672 99.9 0.202 0.199 0.255 RANDOM 26.72
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] -0.02 -0.75 2.56 -2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.886 r_dihedral_angle_4_deg 17.698 r_dihedral_angle_3_deg 14.435 r_dihedral_angle_1_deg 5.258 r_scangle_it 1.973 r_scbond_it 1.169 r_angle_refined_deg 1.114 r_mcangle_it 0.854 r_mcbond_it 0.479 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.886 r_dihedral_angle_4_deg 17.698 r_dihedral_angle_3_deg 14.435 r_dihedral_angle_1_deg 5.258 r_scangle_it 1.973 r_scbond_it 1.169 r_angle_refined_deg 1.114 r_mcangle_it 0.854 r_mcbond_it 0.479 r_nbtor_refined 0.292 r_symmetry_vdw_refined 0.192 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.118 r_chiral_restr 0.068 r_bond_refined_d 0.008 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 5562 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing