X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JATPDB ENTRY 1JAT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7293MCHIP(166-304), UBC13 AND UEV1A WERE COMBINED IN A 1:1:1 MOLAR RATIO, INCUBATED FOR 30 MIN, AND CONCENTRATED TO 10 MG/ML BY ULTRAFILTRATION. CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 20C AGAINST 20% (W/V) PEG2000 MME, 100 MM TRIS-HCL (PH 7.0).
Crystal Properties
Matthews coefficientSolvent content
2.957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.31α = 90
b = 69.991β = 106.95
c = 204.477γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.96096.20.0711.83154327
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)
12.93.0596.60.363.13

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 1JAT2.9196.1249474262195.30.2180.2140.297RANDOM4.56
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_deg40.997
r_dihedral_angle_3_deg26.605
r_dihedral_angle_4_deg21.97
r_dihedral_angle_1_deg14.32
r_angle_refined_deg4.842
r_scangle_it4.096
r_scbond_it2.709
r_mcangle_it1.395
r_mcbond_it0.99
r_symmetry_hbond_refined0.451
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.997
r_dihedral_angle_3_deg26.605
r_dihedral_angle_4_deg21.97
r_dihedral_angle_1_deg14.32
r_angle_refined_deg4.842
r_scangle_it4.096
r_scbond_it2.709
r_mcangle_it1.395
r_mcbond_it0.99
r_symmetry_hbond_refined0.451
r_nbtor_refined0.392
r_nbd_refined0.356
r_symmetry_vdw_refined0.343
r_chiral_restr0.313
r_xyhbond_nbd_refined0.267
r_bond_refined_d0.066
r_gen_planes_refined0.019
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 Atoms11601
Nucleic Acid Atoms
Solvent Atoms35
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing