2FZP

Crystal structure of the USP8 interaction domain of human NRDP1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72981.8M (NH4)2SO4, 0.1M HEPES pH 7.0,0.2M NaCl, 0.001M DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.141.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.796α = 90
b = 44.262β = 90
c = 88.339γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-32005-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM1.00769APS19-BM

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
11.8727.36990.148.974.31210012100-3
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)
11.871.941000.6531.524.41173

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.8727.361095154998.960.1720.169160.23163RANDOM15.627
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]
-0.470.52-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.217
r_dihedral_angle_4_deg18.452
r_dihedral_angle_3_deg13.178
r_scangle_it5.778
r_dihedral_angle_1_deg5.659
r_scbond_it3.809
r_mcangle_it2.51
r_mcbond_it2.045
r_angle_refined_deg1.552
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.217
r_dihedral_angle_4_deg18.452
r_dihedral_angle_3_deg13.178
r_scangle_it5.778
r_dihedral_angle_1_deg5.659
r_scbond_it3.809
r_mcangle_it2.51
r_mcbond_it2.045
r_angle_refined_deg1.552
r_nbtor_refined0.306
r_nbd_refined0.215
r_symmetry_vdw_refined0.203
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_refined0.136
r_chiral_restr0.106
r_bond_refined_d0.017
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1047
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
ARP/wARPmodel building