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Structure of human Heat shock protein 90-alpha N-terminal domain (Hsp90-NTD) variant K112R in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Precipitant: 25 % wt/vol PEG 2000, 200mM MgCl2, 100 mM sodium cacodylate, pH 6.5
Sample: Hsp90a-NTD K112R 20 mg/mL, 10 mM ADP, 500 mM NaCl, 20 mM TRIS, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.04 39.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.917 α = 90 b = 44.729 β = 115.54 c = 54.108 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 PIXEL DECTRIS PILATUS3 6M 2018-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 48.82 96.5 0.034 0.039 0.02 0.999 15.1 3.5 50567 2 16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.41 77.4 0.443 0.543 0.307 0.841 2.1 2.6
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 2XK2 1.34 48.7 47992 2546 96.49 0.13665 0.13506 0.1377 0.169 0.1704 RANDOM 26.372
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] 1.02 0.39 -1.1 -0.21
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.726 r_dihedral_angle_2_deg 34.543 r_dihedral_angle_4_deg 25.855 r_sphericity_bonded 24.677 r_dihedral_angle_3_deg 12.468 r_dihedral_angle_1_deg 6.92 r_rigid_bond_restr 6.829 r_long_range_B_refined 4.394 r_scbond_it 3.172 r_mcangle_it 2.816
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.726 r_dihedral_angle_2_deg 34.543 r_dihedral_angle_4_deg 25.855 r_sphericity_bonded 24.677 r_dihedral_angle_3_deg 12.468 r_dihedral_angle_1_deg 6.92 r_rigid_bond_restr 6.829 r_long_range_B_refined 4.394 r_scbond_it 3.172 r_mcangle_it 2.816 r_mcbond_it 2.273 r_angle_refined_deg 1.975 r_chiral_restr 0.141 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 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 1683 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing