4KYO

Alanine-glyoxylate aminotransferase variant K390A in complex with the TPR domain of human Pex5p


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3R9APDB ENTRY 3R9A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.32930.1 M Bis-Tris (pH=5.3), 0.12 M LiSO4, 17% (w/w) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4750.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.556α = 87.23
b = 74.83β = 83.41
c = 91.751γ = 89.83
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2011-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.812EMBL/DESY, HAMBURGX13

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
12.251.030.1142.673170

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 3R9A2.219.7471036374796.990.177380.175260.21753RANDOM29.249
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]
0.580.99-0.07-0.360.72-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.354
r_dihedral_angle_4_deg19.35
r_dihedral_angle_3_deg15.272
r_dihedral_angle_1_deg5.551
r_angle_refined_deg1.245
r_angle_other_deg0.846
r_chiral_restr0.085
r_bond_refined_d0.008
r_bond_other_d0.005
r_gen_planes_refined0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.354
r_dihedral_angle_4_deg19.35
r_dihedral_angle_3_deg15.272
r_dihedral_angle_1_deg5.551
r_angle_refined_deg1.245
r_angle_other_deg0.846
r_chiral_restr0.085
r_bond_refined_d0.008
r_bond_other_d0.005
r_gen_planes_refined0.004
r_gen_planes_other0.001
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10422
Nucleic Acid Atoms
Solvent Atoms709
Heterogen Atoms86

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling