6RV0

human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma); with PMP in the active site


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529410-12% PEG 6K; 5% 2-methyl-2,4-pentanediol (MPD); 0.1M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
3.4464.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.306α = 90
b = 90.306β = 90
c = 142.071γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9762ESRFID23-1

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
12.747.4999.50.0690.0740.0250.99915.88.516712
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)
12.72.831001.121.1930.4020.7348.4

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 REPLACEMENTTHROUGHOUT5F9S2.747.491591177399.280.26230.25950.3253RANDOM90.111
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]
2.692.69-5.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.09
r_dihedral_angle_4_deg16.845
r_dihedral_angle_3_deg15.785
r_dihedral_angle_1_deg6.848
r_angle_refined_deg1.463
r_angle_other_deg1.21
r_chiral_restr0.06
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.09
r_dihedral_angle_4_deg16.845
r_dihedral_angle_3_deg15.785
r_dihedral_angle_1_deg6.848
r_angle_refined_deg1.463
r_angle_other_deg1.21
r_chiral_restr0.06
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2889
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms16

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction