3CMI

Crystal structure of glutathione-dependent phospholipid peroxidase Hyr1 from the yeast Saccharomyces cerevisiae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62890.2M Ammonium Acetate, 0.1M Sodium Acetate trihydrate, pH4.6, 30% polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3547.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.57α = 90
b = 64.88β = 90
c = 72.02γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2007-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
1239.5693.90.0570.0644.812069230.674
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)
122.1181.50.3360.3763.64.51518

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2P5Q2.0234.683829441868.580.225970.224380.25602RANDOM37.304
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]
1.811.46-3.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.632
r_dihedral_angle_4_deg18.101
r_dihedral_angle_3_deg16.379
r_dihedral_angle_1_deg5.271
r_scangle_it1.234
r_angle_refined_deg1.168
r_scbond_it0.836
r_mcangle_it0.47
r_nbtor_refined0.305
r_mcbond_it0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.632
r_dihedral_angle_4_deg18.101
r_dihedral_angle_3_deg16.379
r_dihedral_angle_1_deg5.271
r_scangle_it1.234
r_angle_refined_deg1.168
r_scbond_it0.836
r_mcangle_it0.47
r_nbtor_refined0.305
r_mcbond_it0.294
r_symmetry_hbond_refined0.24
r_symmetry_vdw_refined0.196
r_nbd_refined0.179
r_xyhbond_nbd_refined0.106
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1150
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing