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Human Cellular Retinoic Acid Binding Protein II (CRABPII) with bound synthetic retinoid DC360.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FR3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 4000, Na Acetate
Crystal Properties Matthews coefficient Solvent content 1.71 28.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.05 α = 90 b = 45.58 β = 102.87 c = 36.67 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 1.0388 Diamond I02
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 1.8 35.77 91.1 6.2 2.6 9030
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 2FR3 1.8 35.77 8554 468 90.56 0.17675 0.17341 0.1825 0.23582 0.2462 RANDOM 22.969
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] 3.98 0.13 -1.57 -2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.927 r_dihedral_angle_4_deg 17.446 r_dihedral_angle_3_deg 15.025 r_long_range_B_refined 7.569 r_long_range_B_other 7.541 r_dihedral_angle_1_deg 6.393 r_scangle_other 3.846 r_mcangle_other 2.792 r_mcangle_it 2.79 r_scbond_other 2.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.927 r_dihedral_angle_4_deg 17.446 r_dihedral_angle_3_deg 15.025 r_long_range_B_refined 7.569 r_long_range_B_other 7.541 r_dihedral_angle_1_deg 6.393 r_scangle_other 3.846 r_mcangle_other 2.792 r_mcangle_it 2.79 r_scbond_other 2.359 r_scbond_it 2.357 r_mcbond_it 1.751 r_mcbond_other 1.745 r_angle_refined_deg 1.681 r_angle_other_deg 0.962 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1078 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 26
Software Software Software Name Purpose iMOSFLM data reduction Aimless data scaling BUCCANEER model building Coot model building REFMAC refinement