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X-Ray Structure Of 1-Deoxy-D-xylulose 5-phosphate Reductoisomerase, DXR, Rv2870c, From Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q0Q PDB ENTRY 1Q0Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP THE SITTING DROPS CONTAINED 1 ML PROTEIN, 5.35 MG/ML, WITH A FINAL CONCENTRATION OF 0.64 MM OF FOSMIDOMYCIN, DISSOLVED IN 10 MM TRIS PH 8.0, AND 1 ML CRYSTALLIZATION BUFFER (40% ETHYLENE GLYCOL, 2 MM MGSO4, 20 MM DTT, 0.2 MM EDTA, AND 100 MM ACETATE PH 5.0). THE RESERVOIR SOLUTION CONSISTED OF A MIXTURE BETWEEN THE CRYSTALLIZATION BUFFER, AND THE BUFFER USED IN THE FINAL STEPS OF THE PROTEIN PURIFICATION (75 MM NACL, 10 MM TRIS-HCL PH 7.5, 20% ETHYLENE GLYCOL, 1 MM MGSO4, 10 MM DTT, 0.1 MM EDTA, AND 50 MM ACETATE PH 5.0). BEFORE THE CRYSTALS WERE FLASH-COOLED IN LIQUID NITROGEN THEY WERE TRANSFERRED TO A DROP WITH THE RESERVOIR SOLUTION COMPLEMENTED WITH AN ADDITIONAL 10% ETHYLENE GLYCOL, AND 1 MM FOSMIDOMYCIN.
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.931 α = 90 b = 56.931 β = 90 c = 238.997 γ = 90
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 2005-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 99.7 0.08 6.2 3.4 56321
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 1.95 99.8 0.39
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 1Q0Q 1.9 40 56321 2962 99.7 0.216 0.215 0.2144 0.247 0.2482 RANDOM 35.13
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] 0.93 0.93 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.689 r_dihedral_angle_4_deg 19.42 r_dihedral_angle_3_deg 12.982 r_dihedral_angle_1_deg 4.949 r_scangle_it 3.004 r_scbond_it 1.838 r_mcangle_it 1.3 r_angle_refined_deg 1.148 r_mcbond_it 0.794 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.689 r_dihedral_angle_4_deg 19.42 r_dihedral_angle_3_deg 12.982 r_dihedral_angle_1_deg 4.949 r_scangle_it 3.004 r_scbond_it 1.838 r_mcangle_it 1.3 r_angle_refined_deg 1.148 r_mcbond_it 0.794 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.078 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 5562 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing