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Crystal structure of chicken CENP-C Cupin domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M lithium citrate, 0.1 M MES-NaOH pH 6.5 and 20% PEG4000
Crystal Properties Matthews coefficient Solvent content 3.12 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.587 α = 90 b = 112.587 β = 90 c = 212.11 γ = 120
Symmetry Space Group P 61 2 2
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 EIGER X 4M 2019-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.99999 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.639 48.75 99.8 0.112 0.118 0.036 0.999 17.8 19.3 24156 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.64 2.77 2.821 2.963 0.902 0.735 19.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2VPV 2.639 47.558 24086 1170 99.76 0.188 0.185 0.2517 0.2298 97.076
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] 0.075 0.037 0.075 -0.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.924 r_dihedral_angle_4_deg 18.646 r_dihedral_angle_3_deg 16.713 r_lrange_it 10.802 r_scangle_it 10.111 r_scbond_it 8.406 r_mcangle_it 8.338 r_dihedral_angle_1_deg 7.702 r_mcbond_it 6.291 r_rigid_bond_restr 2.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.924 r_dihedral_angle_4_deg 18.646 r_dihedral_angle_3_deg 16.713 r_lrange_it 10.802 r_scangle_it 10.111 r_scbond_it 8.406 r_mcangle_it 8.338 r_dihedral_angle_1_deg 7.702 r_mcbond_it 6.291 r_rigid_bond_restr 2.919 r_angle_refined_deg 1.236 r_nbtor_refined 0.306 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.204 r_xyhbond_nbd_refined 0.121 r_symmetry_xyhbond_nbd_refined 0.115 r_chiral_restr 0.086 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3046 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction BUCCANEER phasing