4XDM

N-terminal domain of Hsp90 from Dictyostelium discoideum in complex with Geldanamycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XCJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52900.1 M Hepes, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.8132.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.4α = 90
b = 44.63β = 107.93
c = 60.16γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.95372ESRFBM14

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
11.557.2499.80.04812.54.333584
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)
11.51.581000.6822.24.3

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 REPLACEMENTTHROUGHOUT4XCJ1.557.2431865170399.810.183760.181650.22426RANDOM27.028
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]
-0.56-0.461.28-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.182
r_dihedral_angle_4_deg17.94
r_dihedral_angle_3_deg11.834
r_dihedral_angle_1_deg5.868
r_scangle_it3.434
r_scbond_it2.208
r_mcangle_it1.5
r_angle_refined_deg1.215
r_rigid_bond_restr1.011
r_mcbond_it0.862
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.182
r_dihedral_angle_4_deg17.94
r_dihedral_angle_3_deg11.834
r_dihedral_angle_1_deg5.868
r_scangle_it3.434
r_scbond_it2.208
r_mcangle_it1.5
r_angle_refined_deg1.215
r_rigid_bond_restr1.011
r_mcbond_it0.862
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.005
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_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1677
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement