5DDW

Crystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with the PMP external aldimine adduct with Caerulomycin M


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.2M Sodium acetate, 0.1M TRIS pH 8.5, 32% PEG3350, 2% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.3948.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.788α = 106.63
b = 83.687β = 109.09
c = 88.052γ = 95.07
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-06-22MSINGLE 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)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
12.349.2592.20.1520.0740.9888.14.686965
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3487.50.5550.2960.762.544115

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.349.2582633432392.210.20010.1980.2393RANDOM27.183
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]
0.320.150.080.1-0.22-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.374
r_dihedral_angle_4_deg22.126
r_dihedral_angle_3_deg17.754
r_dihedral_angle_1_deg7.83
r_mcangle_it4.51
r_mcbond_it3.052
r_mcbond_other3.052
r_angle_refined_deg0.703
r_angle_other_deg0.611
r_chiral_restr0.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.374
r_dihedral_angle_4_deg22.126
r_dihedral_angle_3_deg17.754
r_dihedral_angle_1_deg7.83
r_mcangle_it4.51
r_mcbond_it3.052
r_mcbond_other3.052
r_angle_refined_deg0.703
r_angle_other_deg0.611
r_chiral_restr0.065
r_bond_refined_d0.014
r_gen_planes_refined0.014
r_gen_planes_other0.008
r_bond_other_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15813
Nucleic Acid Atoms
Solvent Atoms417
Heterogen Atoms150

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata reduction
MOLREPphasing