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Crystal Structure of the Q108K:K40L:T51V:T53C:Y19W:R58W:T29L:A33W Mutant of Cellular Retinol Binding Protein Type II in Complex with All-trans-Retinal at 1.4 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 2.08 40.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.348 α = 90.04 b = 36.452 β = 94.55 c = 64.265 γ = 116.36
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97918 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 1.4 32.637 49822 49822
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 1.4 1.42 93.5 0.358 2.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2RCQ 1.4 32.637 44292 41479 2368 93.65 0.20159 0.19944 0.24158 0.2477 RANDOM 17.966
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.126 r_dihedral_angle_4_deg 19.892 r_dihedral_angle_3_deg 14.759 r_dihedral_angle_1_deg 6.716 r_scangle_it 6.223 r_scbond_it 4.126 r_mcangle_it 2.864 r_angle_refined_deg 2.434 r_mcbond_it 1.741 r_chiral_restr 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.126 r_dihedral_angle_4_deg 19.892 r_dihedral_angle_3_deg 14.759 r_dihedral_angle_1_deg 6.716 r_scangle_it 6.223 r_scbond_it 4.126 r_mcangle_it 2.864 r_angle_refined_deg 2.434 r_mcbond_it 1.741 r_chiral_restr 0.17 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 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 2153 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 32
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling