2UXS

2.7A crystal structure of inorganic pyrophosphatase (Rv3628) from Mycobacterium tuberculosis at pH 7.5


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52M AMMONIUM SULPHATE, 2% V/V PEG 400, 0.1M HEPES-NA, PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.250

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.022α = 90
b = 102.022β = 90
c = 80.812γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS AND SAGITTAL FOCUSING2005-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.1SRSPX10.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.744980.166.15.6134471.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.8870.631.53.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1FAJ2.7301276166198.60.2340.2320.274RANDOM19.13
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]
0.60.30.6-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.469
r_dihedral_angle_3_deg18.843
r_dihedral_angle_4_deg17.005
r_dihedral_angle_1_deg6.434
r_scangle_it2.341
r_angle_refined_deg1.369
r_scbond_it1.357
r_mcangle_it0.931
r_mcbond_it0.541
r_symmetry_vdw_refined0.483
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.469
r_dihedral_angle_3_deg18.843
r_dihedral_angle_4_deg17.005
r_dihedral_angle_1_deg6.434
r_scangle_it2.341
r_angle_refined_deg1.369
r_scbond_it1.357
r_mcangle_it0.931
r_mcbond_it0.541
r_symmetry_vdw_refined0.483
r_nbtor_refined0.316
r_nbd_refined0.215
r_xyhbond_nbd_refined0.171
r_symmetry_hbond_refined0.142
r_chiral_restr0.104
r_bond_refined_d0.012
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms3828
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing