2ONU

Plasmodium falciparum ubiquitin conjugating enzyme PF10_0330, putative homologue of human UBE2H


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529125% PEG 3350, 0.1 M Ammonium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
4.2170.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.821α = 90
b = 52.821β = 90
c = 206.886γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVVeriMax HR2007-01-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54180

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.385099.70.1020.1027.58.4126261262650.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.382.421000.9610.9612.418.8623

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 1YH62.38501195760899.780.215280.215280.213490.24978RANDOM44.566
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]
1.931.93-3.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.101
r_dihedral_angle_3_deg17.86
r_dihedral_angle_4_deg9.099
r_dihedral_angle_1_deg7.015
r_scangle_it3.249
r_scbond_it2.075
r_mcangle_it1.518
r_angle_refined_deg1.249
r_mcbond_it0.896
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.101
r_dihedral_angle_3_deg17.86
r_dihedral_angle_4_deg9.099
r_dihedral_angle_1_deg7.015
r_scangle_it3.249
r_scbond_it2.075
r_mcangle_it1.518
r_angle_refined_deg1.249
r_mcbond_it0.896
r_nbtor_refined0.307
r_symmetry_vdw_refined0.208
r_nbd_refined0.207
r_symmetry_hbond_refined0.18
r_xyhbond_nbd_refined0.16
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1183
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing