5G09 | pdb_00005g09

The crystal structure of a S-selective transaminase from Bacillus megaterium bound with R-alpha-methylbenzylamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GJUPDB ENTRY 3GJU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.230% PEG300 50 MM NA-PHOSPHATE/CITRATE, PH 4.2 10 MM PYRIDOXAL-5-PHOSPHATE
Crystal Properties
Matthews coefficientSolvent content
2.1843.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.317α = 90
b = 124.593β = 90
c = 126.972γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH MAR-225MM2011-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.944.599.80.09114.4149076-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9298.80.622.54.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3GJU1.944.46141475737999.720.167490.16560.170.203190.2RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.895
r_dihedral_angle_4_deg18.467
r_dihedral_angle_3_deg14.51
r_dihedral_angle_1_deg6.249
r_long_range_B_refined5.213
r_mcangle_it2.427
r_scbond_it2.217
r_mcbond_it1.553
r_angle_refined_deg1.426
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.895
r_dihedral_angle_4_deg18.467
r_dihedral_angle_3_deg14.51
r_dihedral_angle_1_deg6.249
r_long_range_B_refined5.213
r_mcangle_it2.427
r_scbond_it2.217
r_mcbond_it1.553
r_angle_refined_deg1.426
r_chiral_restr0.097
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14809
Nucleic Acid Atoms
Solvent Atoms918
Heterogen Atoms225

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing