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Crystal structure of ATPase domain of Ssb1 chaperone, a member of the HSP70 family, from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YUW PDB entry 1YUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.2 M Magnesium chloride, 0.1 M Tris buffer, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.18 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.543 α = 90 b = 54.504 β = 104.36 c = 90.623 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 2006-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
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 1.92 37.7 98.3 0.077 18.982 4.8 54607 54607 34.7
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 1.92 1.99 86.7 0.54 2.11 3.9
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 PDB entry 1YUW 1.92 37.7 54590 54590 2773 97.74 0.16672 0.16408 0.1733 0.21776 0.221 RANDOM 17.033
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] -1.23 -1.41 -0.15 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.572 r_dihedral_angle_4_deg 18.161 r_dihedral_angle_3_deg 15.71 r_dihedral_angle_1_deg 5.672 r_scangle_it 4.011 r_scbond_it 2.46 r_angle_refined_deg 1.565 r_mcangle_it 1.428 r_angle_other_deg 0.918 r_mcbond_it 0.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.572 r_dihedral_angle_4_deg 18.161 r_dihedral_angle_3_deg 15.71 r_dihedral_angle_1_deg 5.672 r_scangle_it 4.011 r_scbond_it 2.46 r_angle_refined_deg 1.565 r_mcangle_it 1.428 r_angle_other_deg 0.918 r_mcbond_it 0.856 r_mcbond_other 0.273 r_chiral_restr 0.099 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5856 Nucleic Acid Atoms Solvent Atoms 668 Heterogen Atoms 16
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-2000 data reduction MOLREP phasing