3EIY

Crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei with bound pyrophosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.3289100 MM NA/K PHOSPHATE, PH 6.3, 49.5% PEG 200. CRYSTAL 3 MONTHS OLD., pH 6.30, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthew coefficientSolvent content
3.8167.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.952α = 90
b = 100.952β = 90
c = 111.233γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442008-09-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.15098.70.1038.93.619792
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)
12.12.1898.50.6692.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.150195479910.2130.2110.249RANDOM30.12
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]
0.80.40.8-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.57
r_dihedral_angle_4_deg18.89
r_dihedral_angle_3_deg15.203
r_dihedral_angle_1_deg5.857
r_scangle_it3.551
r_scbond_it2.198
r_mcangle_it1.604
r_angle_refined_deg1.46
r_mcbond_it0.89
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.57
r_dihedral_angle_4_deg18.89
r_dihedral_angle_3_deg15.203
r_dihedral_angle_1_deg5.857
r_scangle_it3.551
r_scbond_it2.198
r_mcangle_it1.604
r_angle_refined_deg1.46
r_mcbond_it0.89
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1330
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms39

Software

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