X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UBQPDB ENTRY: 1UBQ, 1X23
experimental modelPDB 1X23PDB ENTRY: 1UBQ, 1X23

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.12920.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.7254.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.646α = 90
b = 102.646β = 90
c = 112.686γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-10-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.0000ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.42598.20.11516.86.198149637-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.43.5299.80.753.33.9955

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: 1UBQ, 1X233.4259612865096298.090.2840.283810.279840.31882RANDOM94.095
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]
-3.19-1.6-3.194.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.848
r_dihedral_angle_3_deg18.909
r_dihedral_angle_4_deg12.395
r_dihedral_angle_1_deg5.313
r_scangle_it1.823
r_mcangle_it1.281
r_scbond_it1.253
r_angle_refined_deg1.013
r_mcbond_it0.834
r_symmetry_vdw_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.848
r_dihedral_angle_3_deg18.909
r_dihedral_angle_4_deg12.395
r_dihedral_angle_1_deg5.313
r_scangle_it1.823
r_mcangle_it1.281
r_scbond_it1.253
r_angle_refined_deg1.013
r_mcbond_it0.834
r_symmetry_vdw_refined0.323
r_nbtor_refined0.302
r_symmetry_hbond_refined0.208
r_nbd_refined0.194
r_xyhbond_nbd_refined0.125
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3986
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms2

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling