5LI3

Crystal structure of HDAC-like protein from P. aeruginosa in complex with a photo-switchable inhibitor.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5G0X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.5M potassium hydrogen phosphate 0.5M sodium hydrogen phosphate 0.1M ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.2344.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.19α = 90
b = 82.19β = 90
c = 217.03γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-09-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0002SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.1321000.240.9886.511.1410432.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.161000.920.842.511.8

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 REPLACEMENTTHROUGHOUT5g0x2.43228611142499.960.226980.224730.27013RANDOM46.624
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]
1.441.44-2.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.925
r_dihedral_angle_4_deg15.919
r_dihedral_angle_3_deg15.087
r_long_range_B_refined6.333
r_long_range_B_other6.319
r_dihedral_angle_1_deg6.024
r_scangle_other3.841
r_mcangle_it3.368
r_mcangle_other3.368
r_scbond_it2.353
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.925
r_dihedral_angle_4_deg15.919
r_dihedral_angle_3_deg15.087
r_long_range_B_refined6.333
r_long_range_B_other6.319
r_dihedral_angle_1_deg6.024
r_scangle_other3.841
r_mcangle_it3.368
r_mcangle_other3.368
r_scbond_it2.353
r_scbond_other2.353
r_mcbond_it2.065
r_mcbond_other2.065
r_angle_refined_deg1.391
r_angle_other_deg1.111
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.003
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5654
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing