2W4B

Epstein-Barr virus alkaline nuclease D203S mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5PROTEIN AT 4.5 MG/ML IN 250 MM NACL, 20MM TRIS PH 7.5, RESERVOIR: 10 MM DTT, 10 MM MGCL2, 0.1M HEPES PH 7.0, 1.5% PEG 400
Crystal Properties
Matthews coefficientSolvent content
360

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.51α = 90
b = 63.787β = 93.59
c = 114.131γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2007-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
13.529.99860.098.531.9213276
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)
13.53.5388.90.174.021.87

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 2W453.531.191297269984.790.193120.189740.2555RANDOM46.332
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]
0.52-0.961.08-1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.065
r_dihedral_angle_3_deg23.834
r_dihedral_angle_4_deg19.75
r_dihedral_angle_1_deg9.206
r_scangle_it3.328
r_angle_refined_deg1.915
r_scbond_it1.801
r_mcangle_it1.472
r_mcbond_it0.757
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.065
r_dihedral_angle_3_deg23.834
r_dihedral_angle_4_deg19.75
r_dihedral_angle_1_deg9.206
r_scangle_it3.328
r_angle_refined_deg1.915
r_scbond_it1.801
r_mcangle_it1.472
r_mcbond_it0.757
r_chiral_restr0.122
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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 Atoms7041
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
TRUNCATEdata scaling