3NET

Crystal structure of histidyl-tRNA synthetase from Nostoc sp. PCC 7120


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52970.2M calicium Acetate, 0.1M Sodium cacodylate, 40% PEG 300, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
3.3963.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.656α = 90
b = 73.656β = 90
c = 521.912γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97937APS19-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
12.75093.10.09529.68.33979438504-3
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)
2.72.721000.6183.679.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.7503841636491192593.10.219260.216850.26545RANDOM71.973
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]
1.461.46-2.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.107
r_dihedral_angle_4_deg18.334
r_dihedral_angle_3_deg16.742
r_dihedral_angle_1_deg5.565
r_scangle_it2.992
r_scbond_it1.766
r_angle_refined_deg1.206
r_mcangle_it1.125
r_rigid_bond_restr0.879
r_mcbond_it0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.107
r_dihedral_angle_4_deg18.334
r_dihedral_angle_3_deg16.742
r_dihedral_angle_1_deg5.565
r_scangle_it2.992
r_scbond_it1.766
r_angle_refined_deg1.206
r_mcangle_it1.125
r_rigid_bond_restr0.879
r_mcbond_it0.59
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6457
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
CNSrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
CNSphasing