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Crystal structure of the amino-terminal domain of HSP90 from Leishmania major, LmjF33.0312:M1-K213
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EKO PDB entry 3EKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 25% PEG 3350, 0.1 M Ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 2 mM AMPPNP, 4 mM MgCl2, 2 mM TCEP, 25% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 51.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.431 α = 90 b = 43.197 β = 90 c = 50.502 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 300 mm CCD 2009-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.96863 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.98 50 94.6 0.072 0.064 34.588 6.2 18169 18169 21.192
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.01 69.6 0.2 0.215 5.42 3.1 650
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 3EKO 2 46.68 17013 17013 933 95.3 0.19762 0.19762 0.19371 0.1911 0.27289 0.2682 RANDOM 27.215
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] -0.24 -0.2 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.941 r_dihedral_angle_4_deg 17.019 r_dihedral_angle_3_deg 16.041 r_dihedral_angle_1_deg 6.164 r_scangle_it 4.281 r_scbond_it 2.642 r_mcangle_it 1.848 r_angle_refined_deg 1.579 r_mcbond_it 1.187 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.941 r_dihedral_angle_4_deg 17.019 r_dihedral_angle_3_deg 16.041 r_dihedral_angle_1_deg 6.164 r_scangle_it 4.281 r_scbond_it 2.642 r_mcangle_it 1.848 r_angle_refined_deg 1.579 r_mcbond_it 1.187 r_nbtor_refined 0.299 r_xyhbond_nbd_refined 0.224 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_metal_ion_refined 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1671 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 61
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling