5MJ7

Structure of the C. elegans nucleoside hydrolase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7.530020 mM Tris, pH 7.5, 150mM NaCl and 2mM DTT
Crystal Properties
Matthews coefficientSolvent content
3.0359.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.578α = 90
b = 84.578β = 90
c = 260.911γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300CCDMAR CCD 165 mm2005-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8075EMBL/DESY, HAMBURGX13

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
11.6524.9396.20.07144.922.4211021826.6
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)
11.651.7176.20.5792.3

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 REPLACEMENTTHROUGHOUTT. b. brucei IG-NH (pdb 3fz0)1.6524.93104702551596.10.138070.137220.15405RANDOM25.385
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]
0.020.02-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.822
r_dihedral_angle_4_deg18.048
r_dihedral_angle_3_deg14.98
r_scangle_it7.83
r_dihedral_angle_1_deg6.712
r_scbond_it4.79
r_mcangle_it2.903
r_mcbond_it1.594
r_angle_refined_deg1.217
r_angle_other_deg1.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.822
r_dihedral_angle_4_deg18.048
r_dihedral_angle_3_deg14.98
r_scangle_it7.83
r_dihedral_angle_1_deg6.712
r_scbond_it4.79
r_mcangle_it2.903
r_mcbond_it1.594
r_angle_refined_deg1.217
r_angle_other_deg1.011
r_mcbond_other0.435
r_chiral_restr0.092
r_gen_planes_refined0.016
r_bond_refined_d0.012
r_gen_planes_other0.006
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms4972
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing