1TFF

Structure of Otubain-2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7288.1514% PEG 4000, 0.1 M HEPES, pH 7.0, 12 % isopropanol and 5 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 288.15K
Crystal Properties
Matthews coefficientSolvent content
2.141.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.433α = 90
b = 65.401β = 90
c = 76.259γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105CCDMARRESEARCHMMAD
21x-ray105CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.97630, 0.97990, 0.98010ESRFBM30A
2SYNCHROTRONESRF BEAMLINE ID14-40.97950ESRFID14-4

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
1,22.110099.70.08518.11271412814128
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)
2.12.181000.2735.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.149.391332070099.510.191250.191250.187920.25689RANDOM26.717
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]
-0.08-0.820.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.707
r_scangle_it6.521
r_scbond_it4.341
r_mcangle_it3.076
r_angle_refined_deg2.382
r_mcbond_it1.792
r_angle_other_deg1.06
r_symmetry_vdw_other0.319
r_nbd_other0.253
r_nbd_refined0.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.707
r_scangle_it6.521
r_scbond_it4.341
r_mcangle_it3.076
r_angle_refined_deg2.382
r_mcbond_it1.792
r_angle_other_deg1.06
r_symmetry_vdw_other0.319
r_nbd_other0.253
r_nbd_refined0.233
r_symmetry_hbond_refined0.218
r_xyhbond_nbd_refined0.187
r_symmetry_vdw_refined0.18
r_chiral_restr0.15
r_nbtor_other0.096
r_bond_refined_d0.028
r_gen_planes_refined0.01
r_gen_planes_other0.007
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1826
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing