X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.5CRYSTALS WERE GROWN BY SETTING-DROP METHOD BY MIXING THE NEDP1-NEDD8 COMPLEX (20MG/ML) WITH EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 20%PEG8000, 200MM NACL, 100MM PHOSPHATE CITRATE PH4.5, pH 4.50
Crystal Properties
Matthews coefficientSolvent content
2.346.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.638α = 90
b = 74.226β = 90
c = 79.59γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.95497.80.085.56.925411
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)
11.91.9583.70.4533

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 DIFFRACTIONMADTHROUGHOUT1.954.2324174130797.80.1710.1690.209RANDOM23.91
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]
-0.371.18-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.274
r_dihedral_angle_4_deg21.851
r_dihedral_angle_3_deg14.12
r_dihedral_angle_1_deg5.679
r_scangle_it4.439
r_scbond_it3.018
r_mcangle_it1.616
r_angle_refined_deg1.569
r_mcbond_it1.099
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.274
r_dihedral_angle_4_deg21.851
r_dihedral_angle_3_deg14.12
r_dihedral_angle_1_deg5.679
r_scangle_it4.439
r_scbond_it3.018
r_mcangle_it1.616
r_angle_refined_deg1.569
r_mcbond_it1.099
r_nbtor_refined0.311
r_symmetry_hbond_refined0.309
r_symmetry_vdw_refined0.218
r_nbd_refined0.203
r_xyhbond_nbd_refined0.196
r_chiral_restr0.109
r_bond_refined_d0.017
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 Atoms2250
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing