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Structure of human Heat shock protein 90-alpha N-terminal domain (Hsp90-NTD) variant K112R in complex with 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, 200mM MgCl2, 100 mM sodium cacodylate, pH 6.5
Sample: Hsp90a-NTD K112R 20 mg/mL, 10 mM AMPCPP, 500 mM NaCl, 20 mM TRIS, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.06 40.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.37 α = 90 b = 41.813 β = 116.35 c = 53.949 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 2.05 48.34 97.1 0.096 0.115 0.062 0.991 8.5 3.1 13159 2 16.3
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 2.05 2.16 98.6 0.4 0.478 0.255 0.81 3 3.1
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 2.05 48.34 12495 654 96.69 0.17644 0.17342 0.1752 0.23822 0.2407 RANDOM 22.594
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 0.03 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.043 r_dihedral_angle_4_deg 25.684 r_dihedral_angle_3_deg 15.094 r_dihedral_angle_1_deg 7.065 r_long_range_B_refined 4.486 r_angle_refined_deg 2.067 r_mcangle_it 1.929 r_scbond_it 1.527 r_mcbond_it 1.256 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.043 r_dihedral_angle_4_deg 25.684 r_dihedral_angle_3_deg 15.094 r_dihedral_angle_1_deg 7.065 r_long_range_B_refined 4.486 r_angle_refined_deg 2.067 r_mcangle_it 1.929 r_scbond_it 1.527 r_mcbond_it 1.256 r_chiral_restr 0.122 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 1810 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing