3CYN

The structure of human GPX8


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72982 M ammonium sulfate, 1.5 % PEG 400, 0.1 M hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7555.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.688α = 90
b = 120.854β = 119.38
c = 75.603γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000SLSX10SA

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
1244.9999.70.0928.94.1476494764929
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)
122.1199.20.3943.14.16901

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2p31244.994524045240240499.570.172170.172170.170730.1989RANDOM26.557
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]
0.220.030.66-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.389
r_dihedral_angle_4_deg14.314
r_dihedral_angle_3_deg13.106
r_dihedral_angle_1_deg6.024
r_scangle_it5.637
r_scbond_it4.361
r_mcangle_it2.636
r_mcbond_it1.985
r_angle_refined_deg1.217
r_angle_other_deg0.892
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.389
r_dihedral_angle_4_deg14.314
r_dihedral_angle_3_deg13.106
r_dihedral_angle_1_deg6.024
r_scangle_it5.637
r_scbond_it4.361
r_mcangle_it2.636
r_mcbond_it1.985
r_angle_refined_deg1.217
r_angle_other_deg0.892
r_mcbond_other0.444
r_symmetry_vdw_other0.236
r_nbd_refined0.195
r_nbd_other0.183
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.166
r_symmetry_vdw_refined0.139
r_symmetry_hbond_refined0.094
r_nbtor_other0.083
r_chiral_restr0.076
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
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 Atoms4203
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing