5DNX

Crystal structure of IGPD from Pyrococcus furiosus in complex with (R)-C348


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62900.1M MES buffer pH 6 and 12% MPD
Crystal Properties
Matthews coefficientSolvent content
2.8456.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.43α = 90
b = 140.43β = 90
c = 136.72γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97950DiamondI04

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
11.848.981000.11822.116.363077
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)
11.81.851001.0064.616.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.848.9859836324199.940.132390.131040.15761RANDOM22.576
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]
0.220.22-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.018
r_scbond_it23.529
r_scbond_other23.524
r_dihedral_angle_4_deg18.235
r_scangle_other17.946
r_long_range_B_refined16.325
r_long_range_B_other16.323
r_dihedral_angle_3_deg11.433
r_mcbond_it8.657
r_mcangle_other7.422
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.018
r_scbond_it23.529
r_scbond_other23.524
r_dihedral_angle_4_deg18.235
r_scangle_other17.946
r_long_range_B_refined16.325
r_long_range_B_other16.323
r_dihedral_angle_3_deg11.433
r_mcbond_it8.657
r_mcangle_other7.422
r_mcbond_other7.389
r_mcangle_it6.777
r_dihedral_angle_1_deg6.474
r_angle_refined_deg1.505
r_angle_other_deg0.88
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.006
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4164
Nucleic Acid Atoms
Solvent Atoms322
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling