5F24

Crystal structure of dual specific IMPase/NADP phosphatase bound with D-inositol-1-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QMF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72980.2M CACL2 2H20, 0.1M HEPES PH 7.0, 15% (W/V) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3246.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.567α = 90
b = 67.835β = 90
c = 137.297γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2012-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.49868.64899.80.1060.1140.04218.97.22027320273
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.6399.90.4970.4970.1991.67.22915

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 REPLACEMENTTHROUGHOUT3QMF2.568.419202103599.680.17530.17220.2329RANDOM31.816
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]
-0.880.860.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.768
r_dihedral_angle_3_deg16.24
r_dihedral_angle_4_deg15.179
r_dihedral_angle_1_deg7.982
r_mcangle_it2.596
r_angle_refined_deg1.832
r_mcbond_it1.556
r_mcbond_other1.554
r_angle_other_deg1.131
r_chiral_restr0.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.768
r_dihedral_angle_3_deg16.24
r_dihedral_angle_4_deg15.179
r_dihedral_angle_1_deg7.982
r_mcangle_it2.596
r_angle_refined_deg1.832
r_mcbond_it1.556
r_mcbond_other1.554
r_angle_other_deg1.131
r_chiral_restr0.113
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.005
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4084
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms94

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing