3FFY

Putative tetrapyrrole (corrin/porphyrin) methyltransferase from Bacteroides fragilis.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52941.26 M ammonium sulfate, 0.1 M acetate buffer, 0.2 M sodium chloride, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.3763.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.536α = 90
b = 60.536β = 90
c = 96.065γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-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
1239.194.10.06740.0879119091190948.1
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)
122.0357.40.7092.087.8355

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT239.1118521185257293.790.2070.2070.2060.231RANDOM34.38
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]
1.841.84-3.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.195
r_dihedral_angle_4_deg20.504
r_dihedral_angle_3_deg19.725
r_dihedral_angle_1_deg6.143
r_scangle_it4.181
r_scbond_it2.541
r_angle_refined_deg1.758
r_mcangle_it1.728
r_angle_other_deg0.962
r_mcbond_it0.916
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.195
r_dihedral_angle_4_deg20.504
r_dihedral_angle_3_deg19.725
r_dihedral_angle_1_deg6.143
r_scangle_it4.181
r_scbond_it2.541
r_angle_refined_deg1.758
r_mcangle_it1.728
r_angle_other_deg0.962
r_mcbond_it0.916
r_mcbond_other0.198
r_chiral_restr0.103
r_bond_refined_d0.02
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms890
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms10

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing