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Structure of human Heat shock protein 90-alpha N-terminal domain (Hsp90-NTD) variant K112A in complex AMPCPP
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 2000,2 200mM MgCl2, 100 mM sodium cacodylate, pH 6.5
Sample: Hsp90a-NTD K112A 20 mg/mL, 10 mM AMPCPP, 500 mM NaCl, 20 mM TRIS, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.11 41.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.777 α = 90 b = 42.034 β = 116.39 c = 54.37 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 0.97622 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 1.75 48.7 99.9 0.067 0.078 0.04 0.997 13.8 3.7 22165 2 10.4
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 1.75 1.84 99.9 0.403 0.472 0.243 0.846 3.6 3.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2XK2 1.75 48.7 21080 1072 99.9 0.16511 0.16321 0.1997 0.1925 RANDOM 18.504
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] -0.04 0.02 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.344 r_dihedral_angle_4_deg 23.16 r_dihedral_angle_3_deg 12.071 r_dihedral_angle_1_deg 6.737 r_long_range_B_refined 5.369 r_angle_refined_deg 2.401 r_scbond_it 1.905 r_mcangle_it 1.875 r_mcbond_it 1.265 r_chiral_restr 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.344 r_dihedral_angle_4_deg 23.16 r_dihedral_angle_3_deg 12.071 r_dihedral_angle_1_deg 6.737 r_long_range_B_refined 5.369 r_angle_refined_deg 2.401 r_scbond_it 1.905 r_mcangle_it 1.875 r_mcbond_it 1.265 r_chiral_restr 0.16 r_bond_refined_d 0.018 r_gen_planes_refined 0.017 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1802 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing