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Crystal Structure of the Q108K:K40L:T51V:T53C:Y19W:R58W:T29L:Q4R Mutant of Cellular Retinol Binding Protein Type II in Complex with All-trans-Retinal at 1.5 Angstrom Resolution
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 EVAPORATION, RECRYSTALLIZATION 4.6 298 40% PEG4000, 0.1 M sodium acetate trihydrate, pH 4.6, 0.1 M ammonium acetate, EVAPORATION, RECRYSTALLIZATION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.05 40.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.918 α = 86.4 b = 35.756 β = 86.44 c = 64.376 γ = 64.94
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD MARMOSAIC 300 mm CCD mirror 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 1.501 32.36 39769 39769
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1.501 32.36 35955 34239 1917 95.23 0.17262 0.17065 0.1737 0.20798 0.2067 RANDOM 16.834
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.88 r_dihedral_angle_4_deg 20.306 r_dihedral_angle_3_deg 13.175 r_dihedral_angle_1_deg 7.412 r_scangle_it 6.115 r_scbond_it 3.986 r_mcangle_it 2.81 r_angle_refined_deg 2.389 r_mcbond_it 1.678 r_chiral_restr 0.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.88 r_dihedral_angle_4_deg 20.306 r_dihedral_angle_3_deg 13.175 r_dihedral_angle_1_deg 7.412 r_scangle_it 6.115 r_scbond_it 3.986 r_mcangle_it 2.81 r_angle_refined_deg 2.389 r_mcbond_it 1.678 r_chiral_restr 0.153 r_bond_refined_d 0.027 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2156 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 48
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling