5EYG

Crystal structure of IMPase/NADP phosphatase complexed with NADP and Ca2+


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.2M CACL2 2H2O, 0.1M BIS-TRIS PH 6.5, 22%(W/V) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.6353.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.089α = 90
b = 78.88β = 90
c = 112.409γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2012-03-05MSINGLE 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
12.264.56999.90.1210.130.04816.47.23320433204
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)
12.22.3299.90.480.480.1931.67.24778

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 REPLACEMENTTHROUGHOUT3QMF2.219.5931471168099.780.16350.16120.2071RANDOM23.678
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]
0.550.4-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.424
r_dihedral_angle_3_deg15.223
r_dihedral_angle_4_deg8.466
r_dihedral_angle_1_deg6.949
r_mcangle_it2.13
r_angle_refined_deg2.111
r_mcbond_it1.345
r_mcbond_other1.343
r_angle_other_deg1.296
r_chiral_restr0.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.424
r_dihedral_angle_3_deg15.223
r_dihedral_angle_4_deg8.466
r_dihedral_angle_1_deg6.949
r_mcangle_it2.13
r_angle_refined_deg2.111
r_mcbond_it1.345
r_mcbond_other1.343
r_angle_other_deg1.296
r_chiral_restr0.117
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.006
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4154
Nucleic Acid Atoms
Solvent Atoms381
Heterogen Atoms164

Software

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