3CC8

Crystal structure of a putative methyltransferase (bce_1332) from bacillus cereus atcc 10987 at 1.64 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277NANODROP, 40.0% MPD, 5.0% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3347.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.223α = 90
b = 54.399β = 109.5
c = 52.751γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2008-01-13MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91837, 0.97964, 0.97978SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.6428.19498.10.0720.0726.53.92930821.775
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.6896.80.7920.7920.93.92099

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 DIFFRACTIONMADTHROUGHOUT1.6428.19429307149197.850.1670.1650.2RANDOM20.725
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]
0.18-1.33-0.19-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.041
r_dihedral_angle_4_deg17.299
r_dihedral_angle_3_deg13.441
r_scangle_it7.574
r_dihedral_angle_1_deg6.478
r_scbond_it5.609
r_mcangle_it3.039
r_mcbond_it2.481
r_angle_refined_deg1.561
r_angle_other_deg0.981
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.041
r_dihedral_angle_4_deg17.299
r_dihedral_angle_3_deg13.441
r_scangle_it7.574
r_dihedral_angle_1_deg6.478
r_scbond_it5.609
r_mcangle_it3.039
r_mcbond_it2.481
r_angle_refined_deg1.561
r_angle_other_deg0.981
r_mcbond_other0.568
r_symmetry_vdw_other0.296
r_nbd_refined0.218
r_symmetry_vdw_refined0.199
r_nbd_other0.187
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.164
r_metal_ion_refined0.149
r_chiral_restr0.105
r_nbtor_other0.087
r_symmetry_hbond_refined0.087
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1664
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction