1Z2U

The 1.1A crystallographic structure of ubiquitin-conjugating enzyme (ubc-2) from Caenorhabditis elegans: functional and evolutionary significance


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QCQpdb entry 1qcq

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1capillary counter-diffusion5277.57mg/mL protein in 2mM sodium citrate, 10% (v/v) ethanol, 1.5M Sodium Chloride, pH 5.0, capillary counter-diffusion, temperature 277.5K
Crystal Properties
Matthews coefficientSolvent content
2.244.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 29.604α = 90
b = 60.457β = 106.45
c = 43.98γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2002-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.97APS22-ID

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
11.13097.40.0555.558674
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)
1.11.1492.60.14335541

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1qcq1.13057952590096.1620.1320.13050.1493RANDOM7.614
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]
0.264-0.1090.037-0.362
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.045
r_dihedral_angle_1_deg14.377
r_dihedral_angle_4_deg13.566
r_dihedral_angle_3_deg12.506
r_sphericity_free6.899
r_scangle_it3.151
r_sphericity_bonded2.914
r_mcangle_it2.548
r_scbond_it2.292
r_mcbond_it1.724
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.045
r_dihedral_angle_1_deg14.377
r_dihedral_angle_4_deg13.566
r_dihedral_angle_3_deg12.506
r_sphericity_free6.899
r_scangle_it3.151
r_sphericity_bonded2.914
r_mcangle_it2.548
r_scbond_it2.292
r_mcbond_it1.724
r_scangle_other1.639
r_mcangle_other1.588
r_angle_refined_deg1.335
r_rigid_bond_restr1.206
r_scbond_other1.041
r_angle_other_deg0.889
r_mcbond_other0.873
r_symmetry_vdw_refined0.386
r_symmetry_vdw_other0.221
r_nbd_refined0.216
r_nbtor_refined0.188
r_nbd_other0.184
r_xyhbond_nbd_refined0.111
r_metal_ion_refined0.111
r_chiral_restr0.086
r_nbtor_other0.086
r_symmetry_hbond_refined0.047
r_symmetry_metal_ion_refined0.024
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1175
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
SCALEPACKdata scaling
MAR345data collection
CNSphasing