3HTZ

Crystal Structure of the catalytic fragment of alanyl-tRNA synthetase in complex with L-serine: Re-refined


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YFSPDB ENTRY 1YFS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.2298PEG 5000 mme, NaCl, Tris-Cl, Tris-base, L-serine, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2244.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.091α = 90
b = 74.091β = 90
c = 173.595γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152004-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.485098.71790717674
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.48

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1YFS2.537.051637788298.70.253270.249990.31531RANDOM40.038
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]
1.281.28-2.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.704
r_dihedral_angle_4_deg18.1
r_dihedral_angle_3_deg15.374
r_dihedral_angle_1_deg4.459
r_mcangle_it0.99
r_angle_refined_deg0.763
r_scangle_it0.678
r_mcbond_it0.609
r_scbond_it0.459
r_nbtor_refined0.325
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.704
r_dihedral_angle_4_deg18.1
r_dihedral_angle_3_deg15.374
r_dihedral_angle_1_deg4.459
r_mcangle_it0.99
r_angle_refined_deg0.763
r_scangle_it0.678
r_mcbond_it0.609
r_scbond_it0.459
r_nbtor_refined0.325
r_xyhbond_nbd_refined0.227
r_nbd_refined0.22
r_symmetry_hbond_refined0.22
r_symmetry_vdw_refined0.186
r_chiral_restr0.053
r_bond_refined_d0.003
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3631
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling