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Zafirlukast in complex with CRM1-Ran-RanBP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CND 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 2.77 55.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.782 α = 90 b = 105.782 β = 90 c = 304.905 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 CCD MARMOSAIC 325 mm CCD 2019-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL18U 0.9792 NFPSS BL18U
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 2.15 304.9 99.2 0.101 0.103 0.021 0.999 23.2 24.7 94712
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 2.15 2.26 95.3 1.393 1.431 0.325 0.797 18.6
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 2.15 50.01 89459 4770 99.19 0.18463 0.18293 0.1969 0.21644 0.2314 RANDOM 57.896
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] -0.22 -0.22 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.978 r_dihedral_angle_4_deg 18.393 r_dihedral_angle_3_deg 15.945 r_long_range_B_refined 7.715 r_long_range_B_other 7.683 r_dihedral_angle_1_deg 6.078 r_scangle_other 3.706 r_mcangle_it 2.697 r_mcangle_other 2.694 r_scbond_it 2.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.978 r_dihedral_angle_4_deg 18.393 r_dihedral_angle_3_deg 15.945 r_long_range_B_refined 7.715 r_long_range_B_other 7.683 r_dihedral_angle_1_deg 6.078 r_scangle_other 3.706 r_mcangle_it 2.697 r_mcangle_other 2.694 r_scbond_it 2.241 r_scbond_other 2.241 r_mcbond_it 1.724 r_mcbond_other 1.721 r_angle_refined_deg 1.31 r_angle_other_deg 0.467 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 10725 Nucleic Acid Atoms Solvent Atoms 536 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing