3BGV

Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with SAH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RI1PDB entry 1RI1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529820% PEG 3350, 0.2 M KCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2144.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.787α = 90
b = 99.672β = 90
c = 167.782γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792996APS19-ID

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
12.35099.90.14127.917.65871658716
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.32.3899.70.6983.3514.85774

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1RI12.349.515520655206294298.920.224860.224860.221220.29448RANDOM34.903
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]
3.6-2.43-1.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.527
r_dihedral_angle_4_deg21.954
r_dihedral_angle_3_deg17.133
r_dihedral_angle_1_deg6.936
r_scangle_it3.825
r_scbond_it2.57
r_mcangle_it1.798
r_angle_refined_deg1.697
r_mcbond_it1.074
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.527
r_dihedral_angle_4_deg21.954
r_dihedral_angle_3_deg17.133
r_dihedral_angle_1_deg6.936
r_scangle_it3.825
r_scbond_it2.57
r_mcangle_it1.798
r_angle_refined_deg1.697
r_mcbond_it1.074
r_nbtor_refined0.308
r_symmetry_hbond_refined0.216
r_nbd_refined0.215
r_xyhbond_nbd_refined0.174
r_symmetry_vdw_refined0.153
r_chiral_restr0.118
r_bond_refined_d0.017
r_gen_planes_refined0.007
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 Atoms8779
Nucleic Acid Atoms
Solvent Atoms476
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing