3K1Z

Crystal Structure of Human Haloacid Dehalogenase-like Hydrolase Domain containing 3 (HDHD3)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.49M NaH2PO4, 0.91M K2HPO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1542.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.625α = 90
b = 62.455β = 90
c = 79.665γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-09-07MSAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9773, 0.9796DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.5543.3299.40.060.0611.54.137908
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.6398.70.5520.55223.619357

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.5543.323596635966189299.270.169350.169350.167440.20688RANDOM10.979
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]
-0.440.060.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.749
r_dihedral_angle_4_deg21.337
r_dihedral_angle_3_deg11.842
r_scangle_it8.284
r_scbond_it5.83
r_dihedral_angle_1_deg5.786
r_mcangle_it3.873
r_mcbond_it2.876
r_angle_refined_deg1.443
r_mcbond_other1.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.749
r_dihedral_angle_4_deg21.337
r_dihedral_angle_3_deg11.842
r_scangle_it8.284
r_scbond_it5.83
r_dihedral_angle_1_deg5.786
r_mcangle_it3.873
r_mcbond_it2.876
r_angle_refined_deg1.443
r_mcbond_other1.148
r_angle_other_deg0.943
r_chiral_restr0.081
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1895
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms10

Software

Software
Software NamePurpose
MAR345data collection
SHELXCDphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling