2IK4

Yeast inorganic pyrophosphatase variant D117E 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
2.5551.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.763α = 90
b = 93.23β = 99.58
c = 69.215γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKUMULTILAYER2001-10-10MSINGLE 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
11.810099.30.0560.0569.83.559558
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)
1.81.8598.10.3230.3232.4

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 REPLACEMENTTHROUGHOUT1HUK1.819.885648230021000.162970.161520.18963RANDOM22.889
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.54
r_scangle_it3.66
r_scbond_it2.263
r_mcangle_it1.443
r_angle_refined_deg1.41
r_angle_other_deg0.82
r_mcbond_it0.805
r_symmetry_vdw_other0.334
r_nbd_other0.245
r_nbd_refined0.219
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.54
r_scangle_it3.66
r_scbond_it2.263
r_mcangle_it1.443
r_angle_refined_deg1.41
r_angle_other_deg0.82
r_mcbond_it0.805
r_symmetry_vdw_other0.334
r_nbd_other0.245
r_nbd_refined0.219
r_symmetry_hbond_refined0.135
r_xyhbond_nbd_refined0.114
r_chiral_restr0.09
r_nbtor_other0.083
r_metal_ion_refined0.059
r_symmetry_vdw_refined0.022
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_gen_planes_other0.006
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_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 Atoms4421
Nucleic Acid Atoms
Solvent Atoms437
Heterogen Atoms10

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
CCP4data scaling