3HXY

Crystal Structure of catalytic fragment of E. coli AlaRS in complex with AMPPCP, Ala-AMP and PCP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.527720% PEG 3350, 0.1 M Tris-HCl, 0.2 M Potassium Nitrate, pH 8.5, vapor diffusion, sitting drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8757.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.355α = 90
b = 108.745β = 90
c = 118.985γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2008-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

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
12.27501000.03765.36810.127449
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)
12.272.3599.90.08510

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.2741.5626016137499.940.18330.180950.22737RANDOM22.077
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]
-0.681.22-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.824
r_dihedral_angle_4_deg13.82
r_dihedral_angle_3_deg12.964
r_dihedral_angle_1_deg5.71
r_scangle_it4.008
r_mcangle_it3.669
r_scbond_it2.814
r_mcbond_it2.561
r_angle_refined_deg1.002
r_chiral_restr0.364
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.824
r_dihedral_angle_4_deg13.82
r_dihedral_angle_3_deg12.964
r_dihedral_angle_1_deg5.71
r_scangle_it4.008
r_mcangle_it3.669
r_scbond_it2.814
r_mcbond_it2.561
r_angle_refined_deg1.002
r_chiral_restr0.364
r_nbtor_refined0.321
r_nbd_refined0.191
r_xyhbond_nbd_refined0.177
r_symmetry_hbond_refined0.163
r_symmetry_vdw_refined0.148
r_metal_ion_refined0.136
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3515
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms84

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection