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Structure of CavAb in complex with nimodipine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MS2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate,100uM nimodipine
Crystal Properties Matthews coefficient Solvent content 5.68 78.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.28 α = 90 b = 125.365 β = 90 c = 191.625 γ = 90
Symmetry Space Group P 21 2 21
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 ADSC QUANTUM 315r 2015-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.9199 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.2 30 99.8 0.112 0.997 15.2 9.3 55285 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.37 99.8 0.686 3.5 9
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 4MS2 3.2 29.79 47933 2456 99.76 0.21906 0.21715 0.2031 0.25572 0.239 RANDOM 105.829
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] 0.25 21.29 -21.53
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 44.414 r_sphericity_free 33.657 r_dihedral_angle_2_deg 32.028 r_dihedral_angle_4_deg 20.071 r_dihedral_angle_3_deg 18.397 r_rigid_bond_restr 11.355 r_scangle_other 11.127 r_mcangle_it 10.74 r_mcangle_other 10.739 r_long_range_B_refined 10.692
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 44.414 r_sphericity_free 33.657 r_dihedral_angle_2_deg 32.028 r_dihedral_angle_4_deg 20.071 r_dihedral_angle_3_deg 18.397 r_rigid_bond_restr 11.355 r_scangle_other 11.127 r_mcangle_it 10.74 r_mcangle_other 10.739 r_long_range_B_refined 10.692 r_long_range_B_other 10.692 r_scbond_it 8.836 r_scbond_other 8.835 r_mcbond_other 8.321 r_mcbond_it 8.319 r_dihedral_angle_1_deg 5.106 r_angle_other_deg 1.883 r_angle_refined_deg 1.664 r_chiral_restr 0.072 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7192 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 189
Software Software Software Name Purpose REFMAC refinement PHENIX refinement HKL-2000 data reduction SCALA data scaling PHASER phasing