3DOU | pdb_00003dou

Crystal structure of methyltransferase involved in cell division from thermoplasma volcanicum gss1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5100MM HEPES,PH 7.5, 20% PEG3350, 10% GLYCEROL, VAPOR DIFFUSION, TEMPERATURE 298K, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
1.9938.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.62α = 90
b = 50.053β = 108.08
c = 56.457γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMAR CCD 165 mm2007-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-IDAPS31-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
11.455099.70.0625.43.830605-5
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)
1.451.598.60.7261.23.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.452028898153899.670.16710.165660.160.194560.19RANDOM20.183
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]
0.150.050.22-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.225
r_dihedral_angle_4_deg17.248
r_dihedral_angle_3_deg13.966
r_dihedral_angle_1_deg11.629
r_scangle_it7.454
r_scbond_it4.901
r_mcangle_it3.669
r_mcbond_it2.742
r_angle_refined_deg1.484
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.225
r_dihedral_angle_4_deg17.248
r_dihedral_angle_3_deg13.966
r_dihedral_angle_1_deg11.629
r_scangle_it7.454
r_scbond_it4.901
r_mcangle_it3.669
r_mcbond_it2.742
r_angle_refined_deg1.484
r_nbtor_refined0.306
r_nbd_refined0.213
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.139
r_symmetry_vdw_refined0.133
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms1489
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms27

Software

Software
Software NamePurpose
SHELXDphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling