2IK1

Yeast inorganic pyrophosphatase variant Y93F with magnesium and phosphate


X-RAY DIFFRACTION

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
2.5752.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.77α = 90
b = 93.541β = 99.88
c = 69.439γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKUMULTILAYER2001-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.710094.40.0650.0657.94.167570
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)
1.71.7694.40.3460.3462.2

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 REPLACEMENTTHROUGHOUT1HUK1.719.696411634171000.167820.166630.19007RANDOM22.081
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.557
r_scangle_it3.749
r_scbond_it2.306
r_angle_refined_deg1.536
r_mcangle_it1.403
r_angle_other_deg0.815
r_mcbond_it0.782
r_symmetry_vdw_other0.33
r_nbd_other0.245
r_nbd_refined0.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.557
r_scangle_it3.749
r_scbond_it2.306
r_angle_refined_deg1.536
r_mcangle_it1.403
r_angle_other_deg0.815
r_mcbond_it0.782
r_symmetry_vdw_other0.33
r_nbd_other0.245
r_nbd_refined0.222
r_symmetry_hbond_refined0.189
r_xyhbond_nbd_refined0.119
r_chiral_restr0.088
r_nbtor_other0.083
r_symmetry_vdw_refined0.057
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms4406
Nucleic Acid Atoms
Solvent Atoms505
Heterogen Atoms15

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
CCP4data scaling