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B28 in complex with CRM1-Ran-RanBP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CND
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 55.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.361 α = 90 b = 106.361 β = 90 c = 304.641 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 2019-12-12 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) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.29 152.35 100 0.186 0.19 0.037 0.995 13.1 26.3 79793
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 2.29 2.35 100 2.518 2.576 0.532 0.957 23.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 7CND 2.29 100.62 75616 3997 99.92 0.19269 0.19116 0.2003 0.2218 0.2269 RANDOM 47.858
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] -0.21 -0.21 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.131 r_dihedral_angle_4_deg 19.196 r_dihedral_angle_3_deg 16.276 r_long_range_B_refined 6.626 r_long_range_B_other 6.61 r_dihedral_angle_1_deg 6.431 r_scangle_other 3.463 r_mcangle_it 2.481 r_mcangle_other 2.481 r_scbond_it 2.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.131 r_dihedral_angle_4_deg 19.196 r_dihedral_angle_3_deg 16.276 r_long_range_B_refined 6.626 r_long_range_B_other 6.61 r_dihedral_angle_1_deg 6.431 r_scangle_other 3.463 r_mcangle_it 2.481 r_mcangle_other 2.481 r_scbond_it 2.086 r_scbond_other 2.085 r_mcbond_it 1.513 r_mcbond_other 1.513 r_angle_refined_deg 1.481 r_angle_other_deg 1.296 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 10734 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing