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Structure of human Heat shock protein 90-alpha N-terminal domain (Hsp90-NTD) variant K112A 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 K112A 20 mg/mL, 10 mM ADP, 500 mM NaCl, 20 mM TRIS, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.21 44.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.948 α = 90 b = 42.135 β = 116.49 c = 54.579 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 2M 2017-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.07227 ESRF ID29
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 1.51 48.29 95.4 0.049 0.057 0.029 0.998 13.6 3.8 32997 2 14.4
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 1.51 1.59 81.9 0.38 0.445 0.228 0.866 2.7 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2XK2 1.51 46.18 31266 1716 95.11 0.1687 0.16696 0.1683 0.20015 0.2021 RANDOM 20.395
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] -0.02 0.01 -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.012 r_dihedral_angle_4_deg 24.059 r_dihedral_angle_3_deg 12.794 r_dihedral_angle_1_deg 6.807 r_long_range_B_refined 5.087 r_angle_refined_deg 2.15 r_mcangle_it 2.096 r_scbond_it 2.074 r_mcbond_it 1.392 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.012 r_dihedral_angle_4_deg 24.059 r_dihedral_angle_3_deg 12.794 r_dihedral_angle_1_deg 6.807 r_long_range_B_refined 5.087 r_angle_refined_deg 2.15 r_mcangle_it 2.096 r_scbond_it 2.074 r_mcbond_it 1.392 r_chiral_restr 0.139 r_gen_planes_refined 0.014 r_bond_refined_d 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1816 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing