2IK9

Yeast inorganic pyrophosphatase variant D152E with magnesium and phosphate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION627716% MPD, 10 MM MGCL2, 1 MM PO4-, PH 6.0, VAPOR DIFFUSION, TEMPERATURE 277K, pH 6.00
Crystal Properties
Matthews coefficientSolvent content
2.5852.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.771α = 90
b = 93.224β = 100.01
c = 70.113γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2001-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM1A0.8000ESRFBM1A

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.510097.70.0350.03533.28.3102428
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.5588.60.1540.1546.5

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 REPLACEMENTTHROUGHOUT1HUK1.519.8797201515097.90.160340.159160.18256RANDOM13.869
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.268
r_dihedral_angle_4_deg14.929
r_dihedral_angle_3_deg11.868
r_dihedral_angle_1_deg6.381
r_scangle_it2.719
r_scbond_it1.956
r_angle_refined_deg1.301
r_mcangle_it1.236
r_mcbond_it0.872
r_angle_other_deg0.776
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.268
r_dihedral_angle_4_deg14.929
r_dihedral_angle_3_deg11.868
r_dihedral_angle_1_deg6.381
r_scangle_it2.719
r_scbond_it1.956
r_angle_refined_deg1.301
r_mcangle_it1.236
r_mcbond_it0.872
r_angle_other_deg0.776
r_symmetry_vdw_other0.29
r_nbd_refined0.226
r_symmetry_vdw_refined0.214
r_symmetry_hbond_refined0.2
r_nbtor_refined0.18
r_nbd_other0.179
r_mcbond_other0.169
r_xyhbond_nbd_refined0.115
r_nbtor_other0.082
r_chiral_restr0.08
r_metal_ion_refined0.055
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
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 AtomsNumber
Protein Atoms4488
Nucleic Acid Atoms
Solvent Atoms759
Heterogen Atoms18

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
CCP4data scaling