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Structure and allosteric regulation of the uridine monophosphate kinase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in-house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.7 291 Na/K Tartrate 1.1 M
HEPES pH 7.7 0.1 M
MPD 2%, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.21 44.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.71 α = 90 b = 175.48 β = 90 c = 65.41 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC QUANTUM 315r 2009-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.918500 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.47 87.7 90.8 0.121 0.044 12.2 4.2 57384 51899 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.6 61.4
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 (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 in-house model 2.54 87.7 53194 43188 2372 86.11 0.20813 0.20474 0.2026 0.26859 0.2568 RANDOM 43.273
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] 0.72 -1.13 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.63 r_dihedral_angle_4_deg 23.843 r_dihedral_angle_3_deg 21.686 r_dihedral_angle_1_deg 7.148 r_scangle_it 1.916 r_angle_refined_deg 1.402 r_scbond_it 1.136 r_mcangle_it 0.932 r_angle_other_deg 0.915 r_mcbond_it 0.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.63 r_dihedral_angle_4_deg 23.843 r_dihedral_angle_3_deg 21.686 r_dihedral_angle_1_deg 7.148 r_scangle_it 1.916 r_angle_refined_deg 1.402 r_scbond_it 1.136 r_mcangle_it 0.932 r_angle_other_deg 0.915 r_mcbond_it 0.506 r_chiral_restr 0.076 r_mcbond_other 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9987 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 217
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling