6GJK

A degradation product of PD 404182 (P2742) bound to Histone Deacetylase-like Amidohydrolase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5G1A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.252930.1 M Malate-Imidazole buffer pH 5.25, 4 % PEG400
Crystal Properties
Matthews coefficientSolvent content
2.7856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.68α = 90
b = 100.68β = 90
c = 175.53γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99988SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.4787.771000.1460.060.99610.613.1152110
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.471.50.4090.791

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 REPLACEMENTTHROUGHOUT5G1A1.4787.77144560745999.940.145910.144420.17446RANDOM16.193
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]
0.340.34-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.494
r_sphericity_free28.362
r_dihedral_angle_4_deg16.825
r_dihedral_angle_3_deg10.767
r_sphericity_bonded10.37
r_dihedral_angle_1_deg6.087
r_long_range_B_refined3.819
r_long_range_B_other3.586
r_scangle_other2.727
r_scbond_it2.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.494
r_sphericity_free28.362
r_dihedral_angle_4_deg16.825
r_dihedral_angle_3_deg10.767
r_sphericity_bonded10.37
r_dihedral_angle_1_deg6.087
r_long_range_B_refined3.819
r_long_range_B_other3.586
r_scangle_other2.727
r_scbond_it2.305
r_scbond_other2.305
r_mcangle_it2.008
r_mcangle_other2.008
r_rigid_bond_restr1.695
r_mcbond_it1.573
r_mcbond_other1.57
r_angle_refined_deg1.462
r_angle_other_deg0.97
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5533
Nucleic Acid Atoms
Solvent Atoms830
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing