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The crystal structure of monomer Q108K:K40L:Y60W CRBPII bound to all-trans-retinal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RCQ PDB entry 2RCQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 294 30% PEG4000, 0.1M CH3COONa.3H2O, pH 4.6, 0.1M CH3COONH4
Crystal Properties Matthews coefficient Solvent content 2.03 39.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.081 α = 90.94 b = 36.049 β = 91.99 c = 63.92 γ = 113.93
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 194 CCD MARMOSAIC 300 mm CCD 2010-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.987 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.5 21.3 92.8 50.3 4.1 41751 41751
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.52 68 3.58
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 PDB entry 2RCQ 1.5 21.3 34422 1855 92.51 0.20076 0.19815 0.1957 0.25071 0.2497 RANDOM 23.022
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.976 r_dihedral_angle_4_deg 18.979 r_dihedral_angle_3_deg 15.976 r_dihedral_angle_1_deg 6.496 r_scangle_it 6.318 r_scbond_it 3.916 r_mcangle_it 2.774 r_angle_refined_deg 2.317 r_mcbond_it 1.652 r_chiral_restr 0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.976 r_dihedral_angle_4_deg 18.979 r_dihedral_angle_3_deg 15.976 r_dihedral_angle_1_deg 6.496 r_scangle_it 6.318 r_scbond_it 3.916 r_mcangle_it 2.774 r_angle_refined_deg 2.317 r_mcbond_it 1.652 r_chiral_restr 0.148 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2152 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement DENZO data reduction HKL-2000 data scaling REFMAC phasing