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Lansoprazole derivative in complex with CRM1-Ran-RanBP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HUF
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 2.75 55.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.888 α = 90 b = 105.888 β = 90 c = 305.588 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 2024-04-22 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) Rpim I (All) 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 50 97.1 0.028 26 20.3 114935
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 0.516
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 32.35 108892 5842 97.04 0.18858 0.18698 0.2001 0.21788 0.2303 RANDOM 48.457
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] -0.62 -0.62 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.421 r_long_range_B_refined 6.1 r_long_range_B_other 5.808 r_dihedral_angle_1_deg 5.769 r_dihedral_angle_2_deg 4.824 r_scangle_other 2.819 r_mcangle_it 2.118 r_mcangle_other 2.118 r_scbond_it 1.63 r_scbond_other 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.421 r_long_range_B_refined 6.1 r_long_range_B_other 5.808 r_dihedral_angle_1_deg 5.769 r_dihedral_angle_2_deg 4.824 r_scangle_other 2.819 r_mcangle_it 2.118 r_mcangle_other 2.118 r_scbond_it 1.63 r_scbond_other 1.63 r_mcbond_it 1.291 r_mcbond_other 1.291 r_angle_refined_deg 1.038 r_angle_other_deg 0.396 r_chiral_restr 0.053 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 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 10749 Nucleic Acid Atoms Solvent Atoms 1173 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing