3LDF

Crystal structure of SMU.776, a putative methyltransferase complexed with SAH


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529320% PEG 8000, 0.1M Na cacodylate pH6.5, 0.2M MgAc2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthew coefficientSolvent content
2.7455.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 165.684α = 90
b = 50.828β = 107.14
c = 59.569γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002005-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.256.1890.750.039910.732.252430622057
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.3371.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2B782.231220503111393.180.176490.173470.23199RANDOM27.061
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]
-0.11-0.14-0.010.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.074
r_dihedral_angle_4_deg20.032
r_dihedral_angle_3_deg16.587
r_dihedral_angle_1_deg7.077
r_scangle_it4.101
r_scbond_it2.712
r_angle_refined_deg1.778
r_mcangle_it1.583
r_mcbond_it0.927
r_chiral_restr0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.074
r_dihedral_angle_4_deg20.032
r_dihedral_angle_3_deg16.587
r_dihedral_angle_1_deg7.077
r_scangle_it4.101
r_scbond_it2.712
r_angle_refined_deg1.778
r_mcangle_it1.583
r_mcbond_it0.927
r_chiral_restr0.133
r_bond_refined_d0.023
r_gen_planes_refined0.008
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_bond_other_d
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3048
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms26

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
MOLREPphasing
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling