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Crystal Structure of the Vps4p-dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XWI PDB ENTRY 1XWI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.9 292 0.1M MES, 0.8M-1.9M MgSO4, pH 5.9-6.5, VAPOR DIFFUSION, temperature 292K
Crystal Properties Matthews coefficient Solvent content 4.14 70.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.116 α = 90 b = 109.116 β = 90 c = 176.632 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 100 CCD MARMOSAIC 225 mm CCD 2005-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 3.35 94.498 99.4 0.057 0.057 22.6 8.1 9446
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 3.35 3.53 100 0.44 0.44 4.9 8.4 1345
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 1XWI 3.35 30 9386 471 99.19 0.27 0.268 0.2991 0.298 0.3378 RANDOM 88.089
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] 2.29 1.15 2.29 -3.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.438 r_dihedral_angle_3_deg 18.419 r_dihedral_angle_4_deg 9.295 r_scangle_it 7.976 r_scbond_it 5.69 r_dihedral_angle_1_deg 5.129 r_mcangle_it 3.813 r_mcbond_it 2.767 r_angle_refined_deg 1.107 r_angle_other_deg 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.438 r_dihedral_angle_3_deg 18.419 r_dihedral_angle_4_deg 9.295 r_scangle_it 7.976 r_scbond_it 5.69 r_dihedral_angle_1_deg 5.129 r_mcangle_it 3.813 r_mcbond_it 2.767 r_angle_refined_deg 1.107 r_angle_other_deg 0.83 r_mcbond_other 0.502 r_nbd_refined 0.26 r_symmetry_vdw_other 0.24 r_nbd_other 0.208 r_nbtor_refined 0.189 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.164 r_symmetry_hbond_refined 0.112 r_xyhbond_nbd_other 0.097 r_nbtor_other 0.09 r_chiral_restr 0.05 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2173 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing CNS refinement PDB_EXTRACT data extraction REFMAC refinement