7NS7

Human L-alanine:glyoxylate aminotransferase minor allele variant: AGXT-Mi (P11L-I340M)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5F9S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52941:1 mixing of: Protein: 0.04M AGT-Mi solution in 0.1M KPhO Precipitant: 0.03M MgCl2 , 0.03M CaCl2 , 0.05M HEPES 0.05M MOPS at a final pH 7.5, 40% v/v Ethylene glycol; 20% w/v PEG 8K
Crystal Properties
Matthews coefficientSolvent content
3.3463.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.59α = 90
b = 90.59β = 90
c = 140.858γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2018-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.000ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.264.0699.60.1090.1250.0610.9929.33.857290
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2699.50.3690.4290.2130.7883.8

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 REPLACEMENTTHROUGHOUT5F9S2.264.0651579566099.520.24550.24070.2894RANDOM26.561
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]
11.6111.61-23.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.16
r_dihedral_angle_4_deg22.376
r_dihedral_angle_3_deg18.42
r_dihedral_angle_1_deg6.715
r_angle_refined_deg1.589
r_angle_other_deg1.412
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.16
r_dihedral_angle_4_deg22.376
r_dihedral_angle_3_deg18.42
r_dihedral_angle_1_deg6.715
r_angle_refined_deg1.589
r_angle_other_deg1.412
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5202
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction