3ELE

Crystal structure of Amino Transferase (RER070207001803) from Eubacterium rectale at 2.10 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72771.0000M LiCl, 20.0000% PEG-6000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3347.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.564α = 82.51
b = 68.387β = 79.52
c = 98.112γ = 75.68
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2008-08-10MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91837,0.97936,0.97917SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
12.129.88197.60.0690.0699.12129210325.239
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1596.70.350.352.126769

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 DIFFRACTIONMADTHROUGHOUT2.129.88192101461097.570.1750.1730.222RANDOM36.74
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]
-1.470.480.22-1.69-1.153.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.234
r_dihedral_angle_4_deg13.839
r_dihedral_angle_3_deg11.051
r_scangle_it3.922
r_dihedral_angle_1_deg3.871
r_scbond_it3.038
r_angle_refined_deg1.618
r_mcangle_it1.602
r_angle_other_deg1.312
r_mcbond_it0.982
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.234
r_dihedral_angle_4_deg13.839
r_dihedral_angle_3_deg11.051
r_scangle_it3.922
r_dihedral_angle_1_deg3.871
r_scbond_it3.038
r_angle_refined_deg1.618
r_mcangle_it1.602
r_angle_other_deg1.312
r_mcbond_it0.982
r_nbd_refined0.167
r_mcbond_other0.163
r_symmetry_hbond_refined0.161
r_nbtor_refined0.156
r_symmetry_vdw_other0.146
r_nbd_other0.137
r_symmetry_vdw_refined0.112
r_xyhbond_nbd_refined0.104
r_chiral_restr0.095
r_nbtor_other0.072
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12432
Nucleic Acid Atoms
Solvent Atoms772
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHARPphasing