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Crystal structure of S.cerevisiae Vps4 in the presence of ATPgammaS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 296 48 % Ethylene glycol, 0.1M Bis-Tris, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 3.22 61.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.956 α = 90 b = 119.804 β = 90 c = 156.831 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 315 2005-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0 NSLS X25
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 3.25 50 100 0.12 8 23550
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.37 100
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 3.25 33 22286 1208 99.7 0.22958 0.2255 0.2426 0.30457 0.287 RANDOM 86.713
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] 0.66 -1.7 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.487 r_dihedral_angle_3_deg 22.443 r_dihedral_angle_4_deg 18.597 r_dihedral_angle_1_deg 7.595 r_scangle_it 2.319 r_angle_refined_deg 1.629 r_scbond_it 1.267 r_mcangle_it 1.17 r_mcbond_it 0.624 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.487 r_dihedral_angle_3_deg 22.443 r_dihedral_angle_4_deg 18.597 r_dihedral_angle_1_deg 7.595 r_scangle_it 2.319 r_angle_refined_deg 1.629 r_scbond_it 1.267 r_mcangle_it 1.17 r_mcbond_it 0.624 r_chiral_restr 0.107 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7327 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 69
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling