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Crystal Structure of S.cerevisiae Vps4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 Sodium Acetate, CdSO4, pH 6.5, temperature 293K, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 3.29 62.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.553 α = 90 b = 86.553 β = 90 c = 236.061 γ = 120
Symmetry Space Group P 65 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 CCD M SINGLE WAVELENGTH 2 1 x-ray CCD M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D 2 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1,2 2.9 50 98.1 0.063 37.5 13.2 12599
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.9 3 99.2 0.606 3.8
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 MAD THROUGHOUT 2.9 10 10792 576 95.1 0.25996 0.25842 0.262 0.28819 0.2927 RANDOM 58.579
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] 2.69 1.34 2.69 -4.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.004 r_dihedral_angle_3_deg 21.48 r_dihedral_angle_4_deg 20.824 r_dihedral_angle_1_deg 5.045 r_scangle_it 1.645 r_angle_refined_deg 1.137 r_scbond_it 1.052 r_mcangle_it 0.945 r_mcbond_it 0.515 r_symmetry_vdw_refined 0.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.004 r_dihedral_angle_3_deg 21.48 r_dihedral_angle_4_deg 20.824 r_dihedral_angle_1_deg 5.045 r_scangle_it 1.645 r_angle_refined_deg 1.137 r_scbond_it 1.052 r_mcangle_it 0.945 r_mcbond_it 0.515 r_symmetry_vdw_refined 0.372 r_nbtor_refined 0.303 r_nbd_refined 0.214 r_metal_ion_refined 0.2 r_symmetry_hbond_refined 0.131 r_xyhbond_nbd_refined 0.105 r_symmetry_metal_ion_refined 0.073 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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_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 2067 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 7
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing REFMAC refinement PDB_EXTRACT data extraction