4XKK

Crystal structure of N-terminal domain of Hsp90 from Dictyostelium discoideum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YES 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52900.1M Hepes, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.8232.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.24α = 90
b = 44.86β = 107.53
c = 60.249γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2007-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU ULTRAX 181.54179

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.739.3199.60.07919.45.65876
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.8599.20.3725.25.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1YES2.728.68558326799.320.220360.218170.27164RANDOM35.793
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]
0.010.070.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.337
r_dihedral_angle_3_deg18.746
r_dihedral_angle_4_deg14.737
r_dihedral_angle_1_deg6.657
r_angle_refined_deg1.129
r_nbtor_refined0.299
r_chiral_restr0.243
r_nbd_refined0.198
r_symmetry_vdw_refined0.152
r_symmetry_hbond_refined0.141
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.337
r_dihedral_angle_3_deg18.746
r_dihedral_angle_4_deg14.737
r_dihedral_angle_1_deg6.657
r_angle_refined_deg1.129
r_nbtor_refined0.299
r_chiral_restr0.243
r_nbd_refined0.198
r_symmetry_vdw_refined0.152
r_symmetry_hbond_refined0.141
r_xyhbond_nbd_refined0.116
r_bond_refined_d0.01
r_gen_planes_refined0.002
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_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1674
Nucleic Acid Atoms
Solvent Atoms27
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement