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Crystal structure of Spc42p, a critical component of spindle pole body in budding yeast
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZTA GCN4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.25 294 100 mM Tris, 200 mM cobalt chloride, 25% PEG 3350, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2 38.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.86 α = 90 b = 57.79 β = 90 c = 57.17 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 4 X4A 2001-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.979 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.97 35 93.9 0.075 0.075 8.2 4.5 10537 9799
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.02 47 0.37 0.37 3.1 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 GCN4 1.97 18.36 10055 9404 475 94.68 0.21565 0.21163 0.2139 0.29655 0.2996 RANDOM 36.772
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] 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.562 r_scbond_it 20.778 r_dihedral_angle_3_deg 19.532 r_dihedral_angle_4_deg 17.793 r_mcangle_it 9.27 r_scangle_it 7.607 r_dihedral_angle_1_deg 5.484 r_angle_refined_deg 1.908 r_mcbond_it 1.842 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.562 r_scbond_it 20.778 r_dihedral_angle_3_deg 19.532 r_dihedral_angle_4_deg 17.793 r_mcangle_it 9.27 r_scangle_it 7.607 r_dihedral_angle_1_deg 5.484 r_angle_refined_deg 1.908 r_mcbond_it 1.842 r_nbtor_refined 0.303 r_xyhbond_nbd_refined 0.271 r_symmetry_hbond_refined 0.266 r_symmetry_vdw_refined 0.251 r_nbd_refined 0.243 r_chiral_restr 0.131 r_metal_ion_refined 0.09 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1065 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing