☰ Navigation Tabs
Human Cellular Retinoic Acid Binding Protein II (CRABPII) with bound synthetic retinoid DC271.
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 PEG5000, TRIS HCL, Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 2.62 53.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.689 α = 90 b = 47.479 β = 90 c = 77.733 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2017-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 40.55 100 2.3 6.3 27170
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 1.53
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 1.5 40.55 25796 1374 99.97 0.14462 0.14292 0.1431 0.17548 0.1758 RANDOM 15.184
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] 0.04 -0.12 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.093 r_sphericity_free 23.255 r_dihedral_angle_4_deg 16.656 r_dihedral_angle_3_deg 11.574 r_sphericity_bonded 11.357 r_dihedral_angle_1_deg 6.881 r_scangle_other 3.318 r_long_range_B_refined 3.177 r_long_range_B_other 3.177 r_scbond_it 2.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.093 r_sphericity_free 23.255 r_dihedral_angle_4_deg 16.656 r_dihedral_angle_3_deg 11.574 r_sphericity_bonded 11.357 r_dihedral_angle_1_deg 6.881 r_scangle_other 3.318 r_long_range_B_refined 3.177 r_long_range_B_other 3.177 r_scbond_it 2.762 r_scbond_other 2.762 r_rigid_bond_restr 2.281 r_mcangle_other 2.006 r_mcangle_it 2 r_angle_refined_deg 1.903 r_mcbond_it 1.533 r_mcbond_other 1.516 r_angle_other_deg 1.133 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1088 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing