3KXO

An orally active inhibitor bound at the active site of HPGDS


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293100mM Tris, pH 8.5, 5mM glutathione, 28-34% PEG 3350, 20-200mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1241.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.799α = 90
b = 78.364β = 91.61
c = 52.455γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2006-08-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.12098.80.06318.12.92308722810-500-123.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1799.30.194.852.82267

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.119.722168921689110498.590.166450.163640.22166RANDOM22.321
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]
0.610.15-0.51-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.71
r_dihedral_angle_4_deg14.763
r_dihedral_angle_3_deg12.65
r_dihedral_angle_1_deg5.415
r_scangle_it1.885
r_scbond_it1.177
r_angle_refined_deg1.057
r_mcangle_it0.985
r_angle_other_deg0.869
r_mcbond_it0.598
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.71
r_dihedral_angle_4_deg14.763
r_dihedral_angle_3_deg12.65
r_dihedral_angle_1_deg5.415
r_scangle_it1.885
r_scbond_it1.177
r_angle_refined_deg1.057
r_mcangle_it0.985
r_angle_other_deg0.869
r_mcbond_it0.598
r_symmetry_vdw_other0.222
r_nbd_refined0.2
r_nbtor_refined0.188
r_nbd_other0.182
r_symmetry_hbond_refined0.123
r_symmetry_vdw_refined0.12
r_xyhbond_nbd_refined0.115
r_mcbond_other0.088
r_nbtor_other0.082
r_chiral_restr0.057
r_metal_ion_refined0.039
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
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 Atoms3276
Nucleic Acid Atoms
Solvent Atoms393
Heterogen Atoms95

Software

Software
Software NamePurpose
MAR345data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing