2XCV

Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with inosine monophosphate and 2,3-bisphosphoglycerate


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 = 91.57α = 90
b = 127.79β = 90
c = 130.61γ = 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
12.32099.40.0717.85.434216-3
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)
12.32.499.50.414.65.6

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 2JCM2.348.6832486172999.420.178930.176270.22868RANDOM35.669
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]
1.161.08-2.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.158
r_dihedral_angle_4_deg20.439
r_dihedral_angle_3_deg16.823
r_dihedral_angle_1_deg6.592
r_scangle_it4.41
r_scbond_it3.059
r_mcangle_it2.021
r_angle_refined_deg1.849
r_mcbond_it1.218
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.158
r_dihedral_angle_4_deg20.439
r_dihedral_angle_3_deg16.823
r_dihedral_angle_1_deg6.592
r_scangle_it4.41
r_scbond_it3.059
r_mcangle_it2.021
r_angle_refined_deg1.849
r_mcbond_it1.218
r_nbtor_refined0.31
r_symmetry_vdw_refined0.236
r_nbd_refined0.209
r_symmetry_hbond_refined0.168
r_xyhbond_nbd_refined0.163
r_chiral_restr0.126
r_metal_ion_refined0.063
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_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 Atoms3767
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing