X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W22PDB ENTRY 1W22

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPHDAC8 POINT MUTANT Y306F, IN 50 MM TRIS-HCL PH 8.0, 5% GLYCEROL, 1 MM DTT, 150 MM KCL, WAS CONCENTRATED TO 217 UM, RESPECTIVELY. Y306F-HDAC8 PLUS 15 MOLAR EXCESSES OF SUBSTRATE, WAS CRYSTALLIZED AT RT BY THE HANGING-DROP METHOD IN 50 MM TRIS-HCL PH 8.0, 50 MM MGCL2, 10% PEG 4,000, 2 MM TRI(2-CARBOXYETHYL)PHOSPHIN (TCEP) AND 30 MM GLYCYL-GLYCYL-GLYCINE.
Crystal Properties
Matthews coefficientSolvent content
2.7254.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.298α = 90
b = 98.694β = 90
c = 110.474γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.2574.5398.70.0916.86.3444262
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)
12.252.3798.10.63.16.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1W222.255041545220398.50.1980.1960.24RANDOM35.83
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]
0.31-3.533.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.467
r_scangle_it2.979
r_scbond_it1.75
r_angle_refined_deg1.42
r_mcangle_it1.261
r_angle_other_deg1.001
r_mcbond_it0.658
r_symmetry_vdw_refined0.331
r_symmetry_hbond_refined0.256
r_nbd_other0.235
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.467
r_scangle_it2.979
r_scbond_it1.75
r_angle_refined_deg1.42
r_mcangle_it1.261
r_angle_other_deg1.001
r_mcbond_it0.658
r_symmetry_vdw_refined0.331
r_symmetry_hbond_refined0.256
r_nbd_other0.235
r_nbd_refined0.227
r_symmetry_vdw_other0.225
r_xyhbond_nbd_refined0.15
r_chiral_restr0.088
r_nbtor_other0.088
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_gen_planes_other0.005
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5613
Nucleic Acid Atoms
Solvent Atoms321
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing