3IEF

Crystal structure of tRNA guanine-n1-methyltransferase from Bartonella henselae using MPCS.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P9P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MPCS7293Initial crystal hit JCSG+ condition G7 15% PEG 3350, 0.1M succinic acid pH 7.0 optimized with microcapillary gradient, MPCS, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.017α = 90
b = 84.467β = 90
c = 97.192γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002009-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.97946SSRLBL7-1

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
12.55099.90.11618.28.916569
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)
2.52.591000.4923.88.51614

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1p9p2.5501652582599.890.1960.1950.225RANDOM30.164
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]
-0.99-1.982.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.112
r_dihedral_angle_4_deg18.305
r_dihedral_angle_3_deg15.455
r_dihedral_angle_1_deg6.039
r_scangle_it3.296
r_scbond_it1.999
r_mcangle_it1.471
r_angle_refined_deg1.381
r_mcbond_it0.78
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.112
r_dihedral_angle_4_deg18.305
r_dihedral_angle_3_deg15.455
r_dihedral_angle_1_deg6.039
r_scangle_it3.296
r_scbond_it1.999
r_mcangle_it1.471
r_angle_refined_deg1.381
r_mcbond_it0.78
r_chiral_restr0.084
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3287
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms

Software

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