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Crystal structure of SPOUT1/CENP-32 | A356N catalytic site mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other using a experimentally determined structure which is currently being processed for deposition (D_1292133583)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.09 M NaF, NaBr, NaI; 0.1 M Sodium HEPES, MOPS (acid) pH 7.5 and 30 % Ethylene glycol, PEG 8K
Crystal Properties Matthews coefficient Solvent content 3.09 60.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.24 α = 90 b = 80.694 β = 90 c = 136.363 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 9M 2014-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92000 Diamond I04-1
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 2.5 37.62 97.33 0.06425 0.07257 0.03278 0.999 11.22 4.5 14321
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 2.5 2.69 0.4695 0.5331 0.2461 0.963 2.72
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 2.5 37.62 13609 711 97.29 0.20546 0.20275 0.2089 0.2623 0.271 RANDOM 84.116
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] 1.83 5.58 -7.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.198 r_long_range_B_refined 10.353 r_long_range_B_other 10.351 r_dihedral_angle_2_deg 9.49 r_dihedral_angle_1_deg 8.163 r_scangle_other 8.094 r_mcangle_it 7.104 r_mcangle_other 7.101 r_scbond_it 5.513 r_scbond_other 5.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.198 r_long_range_B_refined 10.353 r_long_range_B_other 10.351 r_dihedral_angle_2_deg 9.49 r_dihedral_angle_1_deg 8.163 r_scangle_other 8.094 r_mcangle_it 7.104 r_mcangle_other 7.101 r_scbond_it 5.513 r_scbond_other 5.51 r_mcbond_it 4.819 r_mcbond_other 4.816 r_angle_refined_deg 1.701 r_angle_other_deg 0.575 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 2204 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data scaling PHENIX phasing