5CM0

Crystal structure of branched-chain aminotransferase from thermophilic archaea Geoglobus acetivorans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EIY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62930.2M CaCl2, 0.1M Na acetate, 20% isopropanol
Crystal Properties
Matthews coefficientSolvent content
2.7855.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.65α = 90
b = 117.65β = 90
c = 135.98γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.958.8399.60.0660.06831.7519.885638-336.772
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9298.60.7710.7924.02

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 REPLACEMENTTHROUGHOUT2EIY1.9101.8981410422699.640.15330.151430.1879RANDOM37.672
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]
0.480.240.48-1.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.672
r_dihedral_angle_4_deg19.202
r_dihedral_angle_3_deg14.69
r_long_range_B_refined7.276
r_long_range_B_other7.276
r_dihedral_angle_1_deg6.595
r_scangle_other5.802
r_scbond_it4.235
r_scbond_other4.235
r_mcangle_it4.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.672
r_dihedral_angle_4_deg19.202
r_dihedral_angle_3_deg14.69
r_long_range_B_refined7.276
r_long_range_B_other7.276
r_dihedral_angle_1_deg6.595
r_scangle_other5.802
r_scbond_it4.235
r_scbond_other4.235
r_mcangle_it4.163
r_mcangle_other4.163
r_mcbond_it3.384
r_mcbond_other3.384
r_angle_refined_deg1.988
r_angle_other_deg1.144
r_chiral_restr0.136
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6624
Nucleic Acid Atoms
Solvent Atoms626
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction