2VKQ

Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
124% PEG1500, 20% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.652.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.265α = 90
b = 99.388β = 90
c = 78.041γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002006-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.578.0999.70.09155.912172-3
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)
12.52.641000.422.86.2

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 2CN12.5301157357099.50.2110.210.242RANDOM46.09
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]
-1.221.61-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.976
r_dihedral_angle_4_deg21.309
r_dihedral_angle_3_deg13.99
r_dihedral_angle_1_deg5.407
r_scangle_it1.292
r_angle_refined_deg1.039
r_scbond_it0.869
r_angle_other_deg0.82
r_mcangle_it0.466
r_mcbond_it0.399
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.976
r_dihedral_angle_4_deg21.309
r_dihedral_angle_3_deg13.99
r_dihedral_angle_1_deg5.407
r_scangle_it1.292
r_angle_refined_deg1.039
r_scbond_it0.869
r_angle_other_deg0.82
r_mcangle_it0.466
r_mcbond_it0.399
r_xyhbond_nbd_refined0.39
r_symmetry_vdw_other0.246
r_nbd_refined0.204
r_symmetry_vdw_refined0.183
r_nbtor_refined0.173
r_nbd_other0.167
r_symmetry_hbond_refined0.096
r_nbtor_other0.08
r_chiral_restr0.057
r_bond_refined_d0.009
r_gen_planes_refined0.003
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 Atoms2188
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing