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Crystal Structure of the Q108K:K40L Mutant of Cellular Retinol Binding Protein Type II in Complex with All-trans-Retinal at 1.7 Angstrom Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RCQ PDB ENTRY 2RCQ
Crystallization Crystal Properties Matthews coefficient Solvent content 2.02 39.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.814 α = 90.83 b = 35.944 β = 92.88 c = 63.975 γ = 113.19
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 300 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1272 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 1.608 33.016 27686
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 1.608 33.016 27685 1464 92.03 0.21524 0.21236 0.2279 0.26511 0.2708 RANDOM 29.677
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] -0.02 -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.173 r_dihedral_angle_4_deg 19.437 r_dihedral_angle_3_deg 15.268 r_dihedral_angle_1_deg 7.23 r_scangle_it 5.481 r_scbond_it 3.484 r_mcangle_it 2.272 r_angle_refined_deg 1.951 r_mcbond_it 1.345 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.173 r_dihedral_angle_4_deg 19.437 r_dihedral_angle_3_deg 15.268 r_dihedral_angle_1_deg 7.23 r_scangle_it 5.481 r_scbond_it 3.484 r_mcangle_it 2.272 r_angle_refined_deg 1.951 r_mcbond_it 1.345 r_chiral_restr 0.126 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2122 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 33
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling