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KL2.1 in complex with CRM1-Ran-RanBP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.12 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 coefficient Solvent content 2.76 55.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.014 α = 90 b = 106.014 β = 90 c = 305.893 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2023-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9792 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 50 99.6 0.997 3.8 10 78260
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) Redundancy Number Unique Reflections (All) 1 2.3 2.34 95.4 0.567 0.651 0.31 0.288 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 47.44 74217 3949 99.54 0.18815 0.18624 0.1914 0.22418 0.2279 RANDOM 43.963
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] 0.14 0.14 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.532 r_long_range_B_refined 9.894 r_long_range_B_other 9.881 r_dihedral_angle_1_deg 6.191 r_dihedral_angle_2_deg 6.01 r_scangle_other 5.754 r_mcangle_it 4.433 r_mcangle_other 4.433 r_scbond_it 3.49 r_scbond_other 3.489
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.532 r_long_range_B_refined 9.894 r_long_range_B_other 9.881 r_dihedral_angle_1_deg 6.191 r_dihedral_angle_2_deg 6.01 r_scangle_other 5.754 r_mcangle_it 4.433 r_mcangle_other 4.433 r_scbond_it 3.49 r_scbond_other 3.489 r_mcbond_it 2.809 r_mcbond_other 2.809 r_angle_refined_deg 1.134 r_angle_other_deg 0.411 r_chiral_restr 0.055 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 Atoms Number Protein Atoms 10697 Nucleic Acid Atoms Solvent Atoms 680 Heterogen Atoms 195
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing