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Crystal Structure of Yeast Vps74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 8% PEG 3350, 5% ethylene glycol, 50mM MES, 50mM NaCl, 50mM CaCl2, 10mM EGTA, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.82 56.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.688 α = 90 b = 102.688 β = 90 c = 292.323 γ = 120
Symmetry Space Group P 31 2 1
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 300 mm CCD 2007-04-09 M MAD 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2007-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97926, 0.97942, 0.94927 APS 23-ID-D 2 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0360 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 2.8 50 97.4 0.093 11.3 5.2 43558 58.3
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) 2.8 2.9 83.8 0.342 2.8 3658
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 2.8 37.99 43510 2198 96.57 0.237 0.233 0.2337 0.302 0.2983 RANDOM 45.287
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] 1.94 0.97 1.94 -2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.039 r_dihedral_angle_3_deg 21.366 r_dihedral_angle_4_deg 21.033 r_dihedral_angle_1_deg 7.317 r_scangle_it 2.646 r_angle_refined_deg 1.64 r_scbond_it 1.579 r_mcangle_it 1.137 r_mcbond_it 0.617 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.039 r_dihedral_angle_3_deg 21.366 r_dihedral_angle_4_deg 21.033 r_dihedral_angle_1_deg 7.317 r_scangle_it 2.646 r_angle_refined_deg 1.64 r_scbond_it 1.579 r_mcangle_it 1.137 r_mcbond_it 0.617 r_nbtor_refined 0.318 r_nbd_refined 0.244 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.126 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8536 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling SHELXD phasing