1WZV

Crystal Structure of UbcH8


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.3298PEG 3350, calcium acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.449.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.231α = 90
b = 35.486β = 104.55
c = 92.58γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-60402004-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.900SPring-8BL44XU

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
12.110097.70.04616.83.6519900-336.2
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)
2.12.1894.90.237

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1C4Z CHAIN D2.12018854101197.760.209520.209520.206580.26726RANDOM37.989
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]
-1.480.282.03-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.674
r_dihedral_angle_3_deg15.725
r_dihedral_angle_4_deg10.96
r_dihedral_angle_1_deg5.124
r_scangle_it3.595
r_scbond_it2.194
r_mcangle_it1.396
r_angle_refined_deg1.325
r_mcbond_it0.932
r_symmetry_vdw_refined0.337
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.674
r_dihedral_angle_3_deg15.725
r_dihedral_angle_4_deg10.96
r_dihedral_angle_1_deg5.124
r_scangle_it3.595
r_scbond_it2.194
r_mcangle_it1.396
r_angle_refined_deg1.325
r_mcbond_it0.932
r_symmetry_vdw_refined0.337
r_nbtor_refined0.31
r_nbd_refined0.193
r_xyhbond_nbd_refined0.132
r_symmetry_hbond_refined0.112
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2454
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing