2OH7

The Crystal Structure of Cypovirus Polyhedra containing the Human ZIP-kinase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OH6PDB entry 2OH6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1300The crystals used to determine this structure were directly purified from cells, in vivo crystallization in the cytoplasm of the cell, temperature 300K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.742α = 90
b = 102.742β = 90
c = 102.742γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDMAR CCD 165 mmMD2 diffractometer2006-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.99830SLSX06SA

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
12.452099.90.1288.28.267786770-323.4
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)
2.452.5499.40.3483.73.5656

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2OH62.4518.86744673664499.880.1220.1220.1120.221RANDOM17.933
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.486
r_dihedral_angle_4_deg24.078
r_dihedral_angle_3_deg13.976
r_dihedral_angle_1_deg7.383
r_scangle_it2.475
r_angle_refined_deg1.68
r_scbond_it1.667
r_mcangle_it0.947
r_angle_other_deg0.944
r_mcbond_it0.713
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.486
r_dihedral_angle_4_deg24.078
r_dihedral_angle_3_deg13.976
r_dihedral_angle_1_deg7.383
r_scangle_it2.475
r_angle_refined_deg1.68
r_scbond_it1.667
r_mcangle_it0.947
r_angle_other_deg0.944
r_mcbond_it0.713
r_symmetry_vdw_other0.22
r_symmetry_hbond_refined0.21
r_nbd_other0.198
r_nbd_refined0.192
r_symmetry_vdw_refined0.188
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.16
r_mcbond_other0.141
r_chiral_restr0.094
r_nbtor_other0.088
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2007
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms95

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction