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Crystal structure of the SPD-2 domain of human CEP192
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 292.15 100 nl protein solution and 100 nl of reservoir solution which was 0.1 M Na-Acetate pH 5.3, 3.9 M ammonium ni-trate. Crystals were mounted in 0.1 M Na-Acetate pH 4.6, 1 M ammonium nitrate, 30% glycerol.
Crystal Properties Matthews coefficient Solvent content 3.64 66.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.588 α = 90 b = 104.588 β = 90 c = 90.214 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2018-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97835 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.08 90.6 100 0.024 19.7 18.6 33669
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.14 100 0.357 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.08 90.58 32002 1629 99.99 0.21252 0.21197 0.2162 0.22364 0.2287 RANDOM 45.671
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] 0.32 0.16 0.32 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.097 r_dihedral_angle_4_deg 13.437 r_dihedral_angle_3_deg 12.009 r_dihedral_angle_1_deg 6.702 r_long_range_B_refined 4.552 r_long_range_B_other 4.367 r_mcangle_it 2.343 r_mcangle_other 2.343 r_scangle_other 1.673 r_mcbond_other 1.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.097 r_dihedral_angle_4_deg 13.437 r_dihedral_angle_3_deg 12.009 r_dihedral_angle_1_deg 6.702 r_long_range_B_refined 4.552 r_long_range_B_other 4.367 r_mcangle_it 2.343 r_mcangle_other 2.343 r_scangle_other 1.673 r_mcbond_other 1.264 r_mcbond_it 1.263 r_angle_refined_deg 1.171 r_angle_other_deg 1.029 r_scbond_it 0.9 r_scbond_other 0.898 r_chiral_restr 0.036 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2516 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PHENIX refinement iMOSFLM data reduction Aimless data scaling CRANK2 phasing