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The 1.25 A Resolution Structure of Phosphoribosyl-ATP Pyrophosphohydrolase from Mycobacterium tuberculosis, crystal form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y6X PDB entry 1Y6X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1M Sodium formate, 0.1M Sodium iodide, 0.1 mM Calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.702 α = 90 b = 43.119 β = 96.43 c = 67.547 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAC Science DIP-2030 Osmic optics M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE MACSCIENCE 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.79 50 98.9 31912
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 1Y6X 1.79 33.56 31690 1605 99.28 0.209 0.207 0.21 0.256 0.2577 RANDOM 27.448
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] 0.18 -0.25 0.81 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.996 r_dihedral_angle_4_deg 15.784 r_dihedral_angle_3_deg 15.282 r_dihedral_angle_1_deg 5.099 r_scangle_it 3.274 r_scbond_it 2 r_mcangle_it 1.227 r_angle_refined_deg 1.152 r_mcbond_it 0.761 r_symmetry_hbond_refined 0.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.996 r_dihedral_angle_4_deg 15.784 r_dihedral_angle_3_deg 15.282 r_dihedral_angle_1_deg 5.099 r_scangle_it 3.274 r_scbond_it 2 r_mcangle_it 1.227 r_angle_refined_deg 1.152 r_mcbond_it 0.761 r_symmetry_hbond_refined 0.478 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.078 r_metal_ion_refined 0.066 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2708 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction NONIUS/MACSCIENCE data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing