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Dipyridamole binds to the N-terminal domain of human Hsp90A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T0H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M Tris pH8.7,
0.2M MgCl2,
22% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.23 61.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.489 α = 90 b = 89.937 β = 90 c = 99.067 γ = 90
Symmetry Space Group I 2 2 2
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 S 6M 2020-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97852 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.34 36.95 97.4 0.01 0.013 1 32.05 2 13286
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 2.34 2.42 0.06314 0.08929 0.06314 0.988
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 3T0H 2.34 36.95 12625 680 97.38 0.2051 0.2029 0.209 0.2438 0.2487 RANDOM 44.168
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] 0.39 0.6 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.165 r_dihedral_angle_4_deg 22.645 r_dihedral_angle_3_deg 16.428 r_dihedral_angle_1_deg 7.637 r_angle_refined_deg 1.652 r_angle_other_deg 1.329 r_chiral_restr 0.079 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.165 r_dihedral_angle_4_deg 22.645 r_dihedral_angle_3_deg 16.428 r_dihedral_angle_1_deg 7.637 r_angle_refined_deg 1.652 r_angle_other_deg 1.329 r_chiral_restr 0.079 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1644 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 40
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing