3ICA

The crystal structure of the beta subunit of a phenylalanyl-tRNA synthetase from Porphyromonas gingivalis W83


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.2M MgCl2, 0.1M Tris pH8.5, 30% v/v PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
2.3347.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.725α = 90
b = 59.725β = 90
c = 256.266γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMirror2009-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97940APS19-ID

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
12.445099.40.08832.5537.718220
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)
12.442.4893.30.4974.2146859

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 DIFFRACTIONSADTHROUGHOUT2.44501732989199.810.205050.202480.25486RANDOM44.4
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]
1.981.98-3.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.256
r_dihedral_angle_3_deg16.719
r_dihedral_angle_4_deg13.742
r_dihedral_angle_1_deg6.908
r_scangle_it3.655
r_scbond_it2.246
r_mcangle_it1.668
r_angle_refined_deg1.46
r_mcbond_it0.869
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.256
r_dihedral_angle_3_deg16.719
r_dihedral_angle_4_deg13.742
r_dihedral_angle_1_deg6.908
r_scangle_it3.655
r_scbond_it2.246
r_mcangle_it1.668
r_angle_refined_deg1.46
r_mcbond_it0.869
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3304
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms77

Software

Software
Software NamePurpose
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
ARPmodel building
WARPmodel building
HKL-3000phasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling