2OJR

Structure of ubiquitin solved by SAD using the Lanthanide-Binding Tag


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52980.1M HEPES pH 7.5, 3.7 M NaCl, 33% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
4.4872.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.87α = 90
b = 57.87β = 90
c = 115.26γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315SI-111 MONO, MIRRORS2005-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
12.65098.40.12715.88.57214
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)
2.62.6987.70.3782.84.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.630.49614761472851000.2180.2160.254RANDOM48.73
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]
636-8.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.403
r_dihedral_angle_3_deg19.897
r_dihedral_angle_4_deg10.225
r_dihedral_angle_1_deg7.514
r_scangle_it2.171
r_angle_other_deg1.959
r_angle_refined_deg1.608
r_scbond_it1.389
r_mcangle_it0.908
r_mcbond_it0.766
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.403
r_dihedral_angle_3_deg19.897
r_dihedral_angle_4_deg10.225
r_dihedral_angle_1_deg7.514
r_scangle_it2.171
r_angle_other_deg1.959
r_angle_refined_deg1.608
r_scbond_it1.389
r_mcangle_it0.908
r_mcbond_it0.766
r_symmetry_hbond_refined0.32
r_nbd_refined0.286
r_symmetry_vdw_refined0.27
r_symmetry_vdw_other0.267
r_xyhbond_nbd_refined0.258
r_nbd_other0.238
r_nbtor_refined0.196
r_chiral_restr0.18
r_metal_ion_refined0.121
r_nbtor_other0.11
r_mcbond_other0.085
r_bond_refined_d0.013
r_bond_other_d0.008
r_gen_planes_refined0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms871
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms2

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction