2JCM

Crystal structure of Human Cytosolic 5'-Nucleotidase II in complex with beryllium trifluoride


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J2CPDB ENTRY 2J2C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.51.8 M MAGNESIUM SULFATE, 0.1 M TRIS PH 8.5
Crystal Properties
Matthews coefficientSolvent content
3.1661.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.48α = 90
b = 128.26β = 90
c = 131.01γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2006-10-08MSINGLE 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
12.1520980.167.145.241406-3
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)
12.152.299.80.53.365.5

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 2J2C2.1520.6739316208998.10.2130.210.266RANDOM13.27
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]
-0.45-0.470.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.187
r_dihedral_angle_4_deg16.755
r_dihedral_angle_3_deg15.654
r_dihedral_angle_1_deg6.557
r_scangle_it3.526
r_scbond_it2.385
r_angle_refined_deg1.759
r_mcangle_it1.449
r_mcbond_it0.916
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.187
r_dihedral_angle_4_deg16.755
r_dihedral_angle_3_deg15.654
r_dihedral_angle_1_deg6.557
r_scangle_it3.526
r_scbond_it2.385
r_angle_refined_deg1.759
r_mcangle_it1.449
r_mcbond_it0.916
r_nbtor_refined0.313
r_nbd_refined0.21
r_symmetry_vdw_refined0.199
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.152
r_chiral_restr0.117
r_bond_refined_d0.019
r_gen_planes_refined0.007
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 Atoms3812
Nucleic Acid Atoms
Solvent Atoms260
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing