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Crystal structure of human Hsp70 NBD in the ADP- and Mg ion-bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E8A PDB ENTRY 2E8A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1M HEPES-NaOH (pH 7.0), 0.15M MgCl2, 30 % PEG MME 500, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.114 α = 90 b = 63.675 β = 90 c = 143.534 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 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 1.65 50 98.1 0.059 28.8 6.2 50891
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 1.65 1.71 85.7 0.374 2.4
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 2E8A 1.65 20 48203 2586 98.18 0.18746 0.18586 0.21781 0.2186 RANDOM 22.953
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] 0.6 0.23 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.019 r_dihedral_angle_4_deg 19.078 r_dihedral_angle_3_deg 12.465 r_dihedral_angle_1_deg 5.155 r_scangle_it 3.387 r_scbond_it 2.084 r_mcangle_it 1.347 r_angle_refined_deg 1.334 r_mcbond_it 0.741 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.019 r_dihedral_angle_4_deg 19.078 r_dihedral_angle_3_deg 12.465 r_dihedral_angle_1_deg 5.155 r_scangle_it 3.387 r_scbond_it 2.084 r_mcangle_it 1.347 r_angle_refined_deg 1.334 r_mcbond_it 0.741 r_nbtor_refined 0.302 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.09 r_metal_ion_refined 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2938 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 42
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling