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Human Hsp90b nucleotide binding domain in complex with BRI2312
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 21% PEG6000, 0.1M NaCacodylate pH 6.6, 1M Li
Crystal Properties Matthews coefficient Solvent content 2.93 58.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.794 α = 90 b = 90.524 β = 90 c = 97.451 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 EIGER R 1M 2021-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU MICROMAX-003 1.54189
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 1.5 29.21 98.2 0.047 0.052 0.021 0.999 15.5 4.9 46661
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 1.5 1.53 87.7 0.582 0.704 0.385 0.733 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.5 28.841 45618 2286 95.854 0.16 0.159 0.1601 0.1868 0.1881 20.78
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] -0.895 0.319 0.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.264 r_dihedral_angle_3_deg 11.793 r_dihedral_angle_2_deg 8.397 r_lrange_it 6.936 r_lrange_other 6.392 r_dihedral_angle_1_deg 6.382 r_scangle_it 4.981 r_scangle_other 4.979 r_scbond_it 3.173 r_scbond_other 3.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.264 r_dihedral_angle_3_deg 11.793 r_dihedral_angle_2_deg 8.397 r_lrange_it 6.936 r_lrange_other 6.392 r_dihedral_angle_1_deg 6.382 r_scangle_it 4.981 r_scangle_other 4.979 r_scbond_it 3.173 r_scbond_other 3.17 r_mcangle_other 2.829 r_mcangle_it 2.822 r_angle_refined_deg 2.011 r_mcbond_other 1.81 r_mcbond_it 1.809 r_angle_other_deg 0.834 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.176 r_symmetry_nbd_other 0.17 r_nbd_other 0.115 r_symmetry_xyhbond_nbd_refined 0.11 r_chiral_restr 0.096 r_symmetry_nbd_refined 0.083 r_symmetry_nbtor_other 0.075 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1645 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CrysalisPro data reduction PHASER phasing