3BS8

Crystal structure of Glutamate 1-Semialdehyde Aminotransferase complexed with pyridoxamine-5'-phosphate From Bacillus subtilis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GSBPDB ENTRY 3GSB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5295100mM Bicine, 30%(w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9235.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.251α = 90
b = 55.761β = 132.02
c = 80.504γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2006-09-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54179

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
12.359.7610.0715153
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.32.3591061

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3GSB2.3201488077997.080.195470.193420.23362RANDOM24.336
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]
-0.38-0.990.82-1.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.823
r_dihedral_angle_4_deg18.192
r_dihedral_angle_3_deg14.028
r_dihedral_angle_1_deg4.724
r_scangle_it1.452
r_angle_refined_deg1.05
r_scbond_it0.835
r_mcangle_it0.561
r_mcbond_it0.322
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.823
r_dihedral_angle_4_deg18.192
r_dihedral_angle_3_deg14.028
r_dihedral_angle_1_deg4.724
r_scangle_it1.452
r_angle_refined_deg1.05
r_scbond_it0.835
r_mcangle_it0.561
r_mcbond_it0.322
r_nbtor_refined0.308
r_symmetry_vdw_refined0.223
r_nbd_refined0.21
r_symmetry_hbond_refined0.189
r_xyhbond_nbd_refined0.152
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3270
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
AUTOMARdata reduction
MOLREPphasing