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Crystal structure of nucleotide-free human Hsp70 NBD.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ATV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 25 % PEG-3350 W/V, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.39 48.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.129 α = 90 b = 63.7 β = 90 c = 144.118 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 PIXEL DECTRIS PILATUS 6M 2013-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.34 38.35 97.3 0.03823 17.85 3.9 93866
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 1.34 1.39 81.8 0.4752 2.48 3
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 3ATV 1.34 38.35 91861 2000 97.3 0.132 0.131 0.1317 0.154 0.1551 RANDOM 22.46
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] -0.05 0.05
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 55.963 r_dihedral_angle_2_deg 34.951 r_sphericity_bonded 28.344 r_dihedral_angle_4_deg 17.73 r_dihedral_angle_3_deg 12.128 r_long_range_B_refined 7.394 r_rigid_bond_restr 6.679 r_dihedral_angle_1_deg 5.682 r_scbond_it 4.398 r_mcangle_it 2.583
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 55.963 r_dihedral_angle_2_deg 34.951 r_sphericity_bonded 28.344 r_dihedral_angle_4_deg 17.73 r_dihedral_angle_3_deg 12.128 r_long_range_B_refined 7.394 r_rigid_bond_restr 6.679 r_dihedral_angle_1_deg 5.682 r_scbond_it 4.398 r_mcangle_it 2.583 r_mcbond_it 2.205 r_angle_refined_deg 1.998 r_chiral_restr 0.142 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2930 Nucleic Acid Atoms Solvent Atoms 577 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction