2XUP

CRYSTAL STRUCTURE OF the MACHE-Y337A mutant in complex with soaked TZ2PA6 SYN inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5PROTEIN WAS CRYSTALLIZED FROM PEG-600 25-35% (V/V) IN 50-100 MM HEPES, PH 6.0-7.0, OR WITH PEG-550 MME 30% (V/V) IN 50 MM NA ACETATE, PH 7.5
Crystal Properties
Matthews coefficientSolvent content
4.0869.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.743α = 90
b = 110.001β = 90
c = 227.661γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.72099.80.0817.1555109265.9
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)
12.72.8599.80.553.64.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1J062.72053810112199.810.203220.20260.23209RANDOM56.338
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]
3.44.14-7.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.044
r_dihedral_angle_4_deg20.4
r_dihedral_angle_3_deg17.748
r_dihedral_angle_1_deg7.555
r_scangle_it2.419
r_scbond_it1.39
r_angle_refined_deg1.33
r_mcangle_it0.937
r_mcbond_it0.483
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.044
r_dihedral_angle_4_deg20.4
r_dihedral_angle_3_deg17.748
r_dihedral_angle_1_deg7.555
r_scangle_it2.419
r_scbond_it1.39
r_angle_refined_deg1.33
r_mcangle_it0.937
r_mcbond_it0.483
r_chiral_restr0.092
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_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 Atoms8368
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms142

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing