2HAW

Crystal structure of family II Inorganic pyrophosphatase in complex with PNP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WPM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277100mM HEPES/K+ (pH 7.5), 2.3-2.5M ammonium sulphate, 3-4% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.7867.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.011α = 90
b = 115.867β = 90
c = 147.874γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.752099.90.05214.894.2104553104553-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.81000.4522.763.216261

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1WPM1.7519.84993239932352281000.166830.165820.18595RANDOM43.744
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]
-0.741.39-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.399
r_dihedral_angle_3_deg14.627
r_dihedral_angle_4_deg13.727
r_dihedral_angle_1_deg5.787
r_scangle_it4.566
r_mcangle_it3.179
r_scbond_it3.007
r_mcbond_it2.366
r_angle_refined_deg1.519
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.399
r_dihedral_angle_3_deg14.627
r_dihedral_angle_4_deg13.727
r_dihedral_angle_1_deg5.787
r_scangle_it4.566
r_mcangle_it3.179
r_scbond_it3.007
r_mcbond_it2.366
r_angle_refined_deg1.519
r_nbtor_refined0.308
r_nbd_refined0.18
r_symmetry_hbond_refined0.12
r_symmetry_vdw_refined0.118
r_chiral_restr0.116
r_xyhbond_nbd_refined0.114
r_metal_ion_refined0.075
r_bond_refined_d0.016
r_gen_planes_refined0.007
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4744
Nucleic Acid Atoms
Solvent Atoms436
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
XDSdata scaling
CNSphasing