3DMF | pdb_00003dmf

T. Thermophilus 16S rRNA N2 G1207 methyltransferase (RsmC) in complex with AdoMet


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1microbatch technique under oil7.52770.1 M HEPES (pH 7.5) 1.5 M lithium sulfate monohydrate, microbatch technique under oil, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5752.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.697α = 90
b = 88.421β = 90
c = 95.417γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmSlits: Variable vertical and horizontal slits. Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2.5 and 4.5 m. Distance from the monochromator to source is ~10.5 m.2008-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.9797NSLSX4C

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
11.583098.60.05127.35.955718
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)
11.581.6492.40.39834.23766

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.583055718296198.580.18640.184630.180.22020.22RANDOM27.085
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]
0.370.21-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.922
r_dihedral_angle_4_deg17.62
r_dihedral_angle_3_deg12.151
r_dihedral_angle_1_deg5.95
r_scangle_it3.09
r_scbond_it2.029
r_angle_refined_deg1.322
r_mcangle_it1.125
r_mcbond_it0.727
r_nbtor_refined0.304
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2834
Nucleic Acid Atoms
Solvent Atoms632
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing