6JC8

Crystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with amino donor L-Glu


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.52930.2M Sodium acetate, 0.1M TRIS pH 8.5, 32% PEG 3350, 2% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.4249.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.09α = 106.6
b = 83.93β = 109.11
c = 88.459γ = 95.13
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9785SSRFBL19U1

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
12.2549.46950.1220.1410.0710.9928.63.996761
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)
12.252.2995.50.6280.7280.3680.7723.9

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 REPLACEMENTTHROUGHOUT5DDS2.2549.46920484706950.17880.17690.2146RANDOM29.293
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]
0.120.15-0.25-0.31-0.460.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.328
r_dihedral_angle_4_deg20.792
r_dihedral_angle_3_deg15.447
r_dihedral_angle_1_deg6.864
r_angle_refined_deg1.584
r_angle_other_deg1.31
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.328
r_dihedral_angle_4_deg20.792
r_dihedral_angle_3_deg15.447
r_dihedral_angle_1_deg6.864
r_angle_refined_deg1.584
r_angle_other_deg1.31
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15832
Nucleic Acid Atoms
Solvent Atoms548
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing