2JGA

Crystal structure of human cytosolic 5'-nucleotidase III in complex with phosphate and magnesium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CN1PDB ENTRY 2CN1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
124% PEG1500 AND 20% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.459α = 90
b = 101.036β = 90
c = 77.046γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
1377.151000.1124.112.47057
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)
133.161000.426.313

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 2CN13.0150.19670633599.70.1850.1810.268RANDOM44.26
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]
-0.060.23-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.732
r_dihedral_angle_4_deg20.697
r_dihedral_angle_3_deg19.569
r_dihedral_angle_1_deg5.929
r_scangle_it2.17
r_angle_refined_deg1.361
r_scbond_it1.29
r_mcangle_it0.797
r_mcbond_it0.448
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.732
r_dihedral_angle_4_deg20.697
r_dihedral_angle_3_deg19.569
r_dihedral_angle_1_deg5.929
r_scangle_it2.17
r_angle_refined_deg1.361
r_scbond_it1.29
r_mcangle_it0.797
r_mcbond_it0.448
r_nbtor_refined0.31
r_nbd_refined0.222
r_symmetry_vdw_refined0.19
r_symmetry_hbond_refined0.146
r_xyhbond_nbd_refined0.129
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.004
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_refined
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 Atoms2190
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing