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Crystal structure of human Hsp70 NBD in the ADP-, Mg ion-, and K ion-bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ATU PDB ENTRY 3ATU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 293 0.05M calcium chloride, 0.1M bis-tris (pH6.5), 30% PEG MME 550, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.733 α = 90 b = 61.343 β = 90 c = 142.65 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 MARRESEARCH mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.54 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 50 92.5 0.129 10.1349 6.21842 36093
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 87.7 0.523 3.60131
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3ATU 1.75 20 36093 1914 92.14 0.1902 0.18896 0.21275 0.2344 RANDOM 26.317
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] -0.98 3.37 -2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.032 r_dihedral_angle_4_deg 18.491 r_dihedral_angle_3_deg 13.203 r_dihedral_angle_1_deg 5.363 r_scangle_it 4.198 r_scbond_it 2.508 r_mcangle_it 1.475 r_angle_refined_deg 1.412 r_mcbond_it 0.793 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.032 r_dihedral_angle_4_deg 18.491 r_dihedral_angle_3_deg 13.203 r_dihedral_angle_1_deg 5.363 r_scangle_it 4.198 r_scbond_it 2.508 r_mcangle_it 1.475 r_angle_refined_deg 1.412 r_mcbond_it 0.793 r_nbtor_refined 0.305 r_nbd_refined 0.204 r_metal_ion_refined 0.2 r_symmetry_vdw_refined 0.158 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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_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 2938 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling