2XCW

Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with inosine monophosphate and ATP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JCMPDB ENTRY 2JCM

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.1661

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.56α = 90
b = 127.44β = 90
c = 130.44γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MDYNAMICALLY BENDABLE2008-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.92099.90.05215.560260-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.921000.414.485.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2JCM1.92057151304699.930.168140.166760.19357RANDOM33.823
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]
0.94-0.11-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.278
r_dihedral_angle_4_deg19.228
r_dihedral_angle_3_deg14.123
r_dihedral_angle_1_deg5.937
r_scangle_it3.133
r_scbond_it2.316
r_angle_refined_deg1.557
r_mcangle_it1.257
r_mcbond_it1.087
r_angle_other_deg0.953
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.278
r_dihedral_angle_4_deg19.228
r_dihedral_angle_3_deg14.123
r_dihedral_angle_1_deg5.937
r_scangle_it3.133
r_scbond_it2.316
r_angle_refined_deg1.557
r_mcangle_it1.257
r_mcbond_it1.087
r_angle_other_deg0.953
r_symmetry_vdw_other0.312
r_symmetry_vdw_refined0.218
r_nbd_refined0.204
r_nbd_other0.194
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.164
r_symmetry_hbond_refined0.133
r_chiral_restr0.096
r_nbtor_other0.085
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3828
Nucleic Acid Atoms
Solvent Atoms409
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing