2Y6V

Peroxisomal alpha-beta-hydrolase Lpx1 (Yor084w) from Saccharomyces cerevisiae (crystal form I)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION293HANGING OR SITTING DROP VAPOR DIFFUSION AT 20 DEGREES CELSIUS. 4 UL OF PROTEIN (7.9 MG/ML) MIXED WITH 2UL RESERVOIR (0.1 M HEPES, PH 7.5, 10 % PEG 8000).
Crystal Properties
Matthews coefficientSolvent content
2.958

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.48α = 90
b = 87.77β = 95.1
c = 125.04γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCDVARIMAX HF CONFOCAL2008-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.832095.60.09153.634876-336.5
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)
12.832.968.40.42.972.4

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 REPLACEMENTTHROUGHOUTENSEMBLE OF TEN ALPHA-BETA HYDROLASES AS POLY-ALA MODELS TRIMMED TO THE COMMON CORE.2.8319.753313117441000.209380.207070.25408RANDOM32.557
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]
0.190.24-0.350.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.289
r_dihedral_angle_1_deg18.628
r_dihedral_angle_4_deg17.662
r_dihedral_angle_3_deg15.396
r_angle_refined_deg1.475
r_scangle_it1.294
r_angle_other_deg0.967
r_scbond_it0.913
r_mcangle_it0.553
r_mcbond_it0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.289
r_dihedral_angle_1_deg18.628
r_dihedral_angle_4_deg17.662
r_dihedral_angle_3_deg15.396
r_angle_refined_deg1.475
r_scangle_it1.294
r_angle_other_deg0.967
r_scbond_it0.913
r_mcangle_it0.553
r_mcbond_it0.304
r_mcbond_other0.143
r_chiral_restr0.08
r_bond_refined_d0.016
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8786
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing