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Crystal structure of mouse DCAR2 CRD domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 PEG
Crystal Properties Matthews coefficient Solvent content 4 69.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.979 α = 90 b = 72.435 β = 90 c = 101.106 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 CCD ADSC QUANTUM 210 2018-12-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.84 58.9 99.7 0.12 15.1 7.2 22002
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.44 0.687 0.867 2.99
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6LFJ 2.304 43.971 22002 1141 99.724 0.19 0.1888 0.1951 0.2207 0.2268 34.626
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] 0.237 -0.178 -0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.397 r_dihedral_angle_3_deg 15.537 r_lrange_it 12.208 r_lrange_other 12.201 r_dihedral_angle_4_deg 11.376 r_scangle_it 7.691 r_scangle_other 7.689 r_dihedral_angle_1_deg 6.94 r_mcangle_it 5.777 r_mcangle_other 5.775
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.397 r_dihedral_angle_3_deg 15.537 r_lrange_it 12.208 r_lrange_other 12.201 r_dihedral_angle_4_deg 11.376 r_scangle_it 7.691 r_scangle_other 7.689 r_dihedral_angle_1_deg 6.94 r_mcangle_it 5.777 r_mcangle_other 5.775 r_scbond_it 5.015 r_scbond_other 5.013 r_mcbond_it 3.754 r_mcbond_other 3.742 r_angle_other_deg 2.37 r_angle_refined_deg 1.407 r_symmetry_nbd_refined 0.29 r_nbd_other 0.229 r_symmetry_nbd_other 0.216 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.171 r_metal_ion_refined 0.09 r_symmetry_xyhbond_nbd_refined 0.078 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.064 r_bond_other_d 0.036 r_bond_refined_d 0.007 r_gen_planes_other 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2172 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing