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Crystal structure of SPOUT1/CENP-32 bound to SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other using an experimentally determined model currently being processed for deposition (D_1292133583)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.06 M MgCl2, CaCl2 or 0.09 M NaF, NaBr, NaI with 0.1 M Imidazole, MES (acid) pH 6.5 and 30 % Ethylene glycol, PEG 8K
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.07 α = 90 b = 80.83 β = 90 c = 135.69 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 XE 16M 2014-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97000 Diamond I03
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 2.62 55.01 99.08 0.08553 0.0932 0.0365 0.998 16.11 6.5 12626
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 2.62 2.88 98.02 0.6634 0.7196 0.2761 0.947 3.81 6.6
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 MOLECULAR REPLACEMENT THROUGHOUT 2.62 55.01 12000 628 99.09 0.20662 0.2028 0.2083 0.2802 0.2763 RANDOM 83.661
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] 4.02 3.72 -7.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.501 r_dihedral_angle_2_deg 10.633 r_long_range_B_refined 9.332 r_long_range_B_other 9.33 r_dihedral_angle_1_deg 7.886 r_scangle_other 7.166 r_mcangle_it 6.573 r_mcangle_other 6.571 r_scbond_it 4.783 r_scbond_other 4.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.501 r_dihedral_angle_2_deg 10.633 r_long_range_B_refined 9.332 r_long_range_B_other 9.33 r_dihedral_angle_1_deg 7.886 r_scangle_other 7.166 r_mcangle_it 6.573 r_mcangle_other 6.571 r_scbond_it 4.783 r_scbond_other 4.781 r_mcbond_other 4.376 r_mcbond_it 4.375 r_angle_refined_deg 1.583 r_angle_other_deg 0.524 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2151 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data scaling PHENIX phasing