8ITV

KL2.1 in complex with CRM1-Ran-RanBP1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8HQ6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.12 M Monosaccharides (20 mM D-Glucose; 20 mM D-Mannose; 20 mM D-Galactose; 20 mM L-Fucose; 20 mM D-Xylose; 20 mM N-Acetyl-D-Glucosamine), 0.1 M buffer system 1 pH 6.5 (sodium HEPES and MOPS), and 50 % Precipitant Mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000)
Crystal Properties
Matthews coefficientSolvent content
2.7655.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.014α = 90
b = 106.014β = 90
c = 305.893γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2023-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.9792SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.35099.60.9973.81078260
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3495.40.5670.6510.310.2883.8

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 REPLACEMENTTHROUGHOUT2.347.4474217394999.540.188150.186240.22418RANDOM43.963
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]
0.140.14-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.532
r_long_range_B_refined9.894
r_long_range_B_other9.881
r_dihedral_angle_1_deg6.191
r_dihedral_angle_2_deg6.01
r_scangle_other5.754
r_mcangle_it4.433
r_mcangle_other4.433
r_scbond_it3.49
r_scbond_other3.489
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.532
r_long_range_B_refined9.894
r_long_range_B_other9.881
r_dihedral_angle_1_deg6.191
r_dihedral_angle_2_deg6.01
r_scangle_other5.754
r_mcangle_it4.433
r_mcangle_other4.433
r_scbond_it3.49
r_scbond_other3.489
r_mcbond_it2.809
r_mcbond_other2.809
r_angle_refined_deg1.134
r_angle_other_deg0.411
r_chiral_restr0.055
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10697
Nucleic Acid Atoms
Solvent Atoms680
Heterogen Atoms195

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing