8CMS

OTUB2 in covalent complex with LN5P45


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5QIO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320 %v/v 2-Propanol 13 %w/v PEG 4K 0.1 M HEPES pH 8
Crystal Properties
Matthews coefficientSolvent content
2.2745.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.65α = 90
b = 45.25β = 96.05
c = 58γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2020-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.7747.4399.60.1180.1420.0770.99473.224095
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.8199.61.2950.9850.3380.72.7

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.7747.4324082122999.5910.2120.20990.252125.72
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]
0.805-0.657-0.279-0.378
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.263
r_dihedral_angle_4_deg16.98
r_dihedral_angle_3_deg16.396
r_dihedral_angle_other_3_deg8.61
r_dihedral_angle_1_deg6.988
r_lrange_other6.633
r_lrange_it6.628
r_scangle_it5.37
r_scangle_other5.368
r_scbond_it3.399
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.263
r_dihedral_angle_4_deg16.98
r_dihedral_angle_3_deg16.396
r_dihedral_angle_other_3_deg8.61
r_dihedral_angle_1_deg6.988
r_lrange_other6.633
r_lrange_it6.628
r_scangle_it5.37
r_scangle_other5.368
r_scbond_it3.399
r_scbond_other3.398
r_mcangle_it3.186
r_mcangle_other3.18
r_mcbond_it2.12
r_mcbond_other2.103
r_angle_refined_deg1.654
r_angle_other_deg1.408
r_symmetry_nbd_refined0.373
r_symmetry_xyhbond_nbd_refined0.223
r_nbd_refined0.218
r_nbd_other0.215
r_nbtor_refined0.18
r_symmetry_nbd_other0.177
r_xyhbond_nbd_refined0.15
r_symmetry_xyhbond_nbd_other0.123
r_chiral_restr0.081
r_symmetry_nbtor_other0.078
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1857
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing