2BKQ

NEDD8 protease


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9NEDP1 (14MG/ML) WITH EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 0.1M BICINE PH9.0, 30% PEG3000., pH 9.00
Crystal Properties
Matthews coefficientSolvent content
2.3447.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.07α = 99.74
b = 57.51β = 110.95
c = 74.996γ = 92.41
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
126796.70.059.8254875
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)
122.0595.70.2531.9

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 REPLACEMENTTHROUGHOUT269.0154258288296.90.1960.1930.25RANDOM24.72
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]
1.551.470.99-1.510.570.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.975
r_dihedral_angle_4_deg17.453
r_dihedral_angle_3_deg16.303
r_dihedral_angle_1_deg6.035
r_scangle_it3.429
r_scbond_it2.386
r_angle_refined_deg1.509
r_mcangle_it1.434
r_mcbond_it0.857
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.975
r_dihedral_angle_4_deg17.453
r_dihedral_angle_3_deg16.303
r_dihedral_angle_1_deg6.035
r_scangle_it3.429
r_scbond_it2.386
r_angle_refined_deg1.509
r_mcangle_it1.434
r_mcbond_it0.857
r_nbtor_refined0.313
r_nbd_refined0.227
r_symmetry_vdw_refined0.197
r_xyhbond_nbd_refined0.179
r_symmetry_hbond_refined0.138
r_chiral_restr0.112
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6631
Nucleic Acid Atoms
Solvent Atoms386
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling