2ZIM

Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5289100 MM TRIS, 10% PEG2000-MME, pH 7.5, VAPOR DIFFUSION, temperature 289 K
Crystal Properties
Matthews coefficientSolvent content
3.3563.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.07α = 90
b = 105.07β = 90
c = 70.262γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2007-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEOTHER1.514

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
12.1400.08726.111.22591011
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.18100

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.134.424560131199.920.188450.186270.22811RANDOM45.032
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]
-0.42-0.21-0.420.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.348
r_dihedral_angle_4_deg20.025
r_dihedral_angle_3_deg15.53
r_dihedral_angle_1_deg7.036
r_scangle_it4.819
r_scbond_it3.095
r_mcangle_it2.173
r_angle_refined_deg1.835
r_mcbond_it1.339
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.348
r_dihedral_angle_4_deg20.025
r_dihedral_angle_3_deg15.53
r_dihedral_angle_1_deg7.036
r_scangle_it4.819
r_scbond_it3.095
r_mcangle_it2.173
r_angle_refined_deg1.835
r_mcbond_it1.339
r_nbtor_refined0.308
r_symmetry_hbond_refined0.23
r_nbd_refined0.215
r_symmetry_vdw_refined0.183
r_xyhbond_nbd_refined0.178
r_chiral_restr0.135
r_bond_refined_d0.02
r_gen_planes_refined0.008
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_refined
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 Atoms2116
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
CCP4phasing