6ELW

High resolution structure of selenocysteine containing human GPX4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OBI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529330 % (w/v) PEG 1500, 10 % (v/v) isopropanol, 0.1 M calcium chloride and 0.1 M imidazole/ hydrochloric acid pH 6.5
Crystal Properties
Matthews coefficientSolvent content
1.727.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.963α = 90
b = 69β = 115.12
c = 35.666γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2MMirror2015-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

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
11.334.5299.60.0988.54.735608
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)
11.31.3291.90.56924.1

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 REPLACEMENTTHROUGHOUT2OBI1.334.5233903167899.580.125260.12380.15541RANDOM13.116
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]
0.190.53-0.720.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.271
r_sphericity_free25.895
r_dihedral_angle_4_deg17.694
r_dihedral_angle_3_deg11.868
r_sphericity_bonded8.448
r_dihedral_angle_1_deg5.886
r_long_range_B_refined4.55
r_long_range_B_other3.708
r_scangle_other2.505
r_scbond_it2.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.271
r_sphericity_free25.895
r_dihedral_angle_4_deg17.694
r_dihedral_angle_3_deg11.868
r_sphericity_bonded8.448
r_dihedral_angle_1_deg5.886
r_long_range_B_refined4.55
r_long_range_B_other3.708
r_scangle_other2.505
r_scbond_it2.073
r_scbond_other2.072
r_rigid_bond_restr1.641
r_angle_refined_deg1.573
r_mcangle_other1.537
r_mcangle_it1.536
r_angle_other_deg1.201
r_mcbond_it1.185
r_mcbond_other1.153
r_chiral_restr0.108
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1320
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing