3E05

CRYSTAL STRUCTURE OF Precorrin-6y C5,15-methyltransferase FROM Geobacter metallireducens GS-15


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72941800MM AMMONIUM TRI-CITRATE, PH 7.0, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
2.1442.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.71α = 90
b = 83.451β = 95.72
c = 149.056γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2008-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
11.765092.30.077.43.6151124-532.206
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)
11.761.8257.30.910.910.52.7

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 DIFFRACTIONSADTHROUGHOUT1.820130412403895.540.21710.215720.26179RANDOM40.223
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]
-0.660.461.72-0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.905
r_dihedral_angle_4_deg21.2
r_dihedral_angle_3_deg15.96
r_scangle_it6.973
r_dihedral_angle_1_deg6.202
r_scbond_it4.84
r_mcangle_it4.409
r_mcbond_it3.115
r_angle_refined_deg1.309
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.905
r_dihedral_angle_4_deg21.2
r_dihedral_angle_3_deg15.96
r_scangle_it6.973
r_dihedral_angle_1_deg6.202
r_scbond_it4.84
r_mcangle_it4.409
r_mcbond_it3.115
r_angle_refined_deg1.309
r_nbtor_refined0.303
r_symmetry_hbond_refined0.185
r_nbd_refined0.161
r_xyhbond_nbd_refined0.151
r_symmetry_vdw_refined0.134
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11831
Nucleic Acid Atoms
Solvent Atoms537
Heterogen Atoms20

Software

Software
Software NamePurpose
SHELXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing