1VQ1

Crystal structure of N5-glutamine methyltransferase, HemK(EC 2.1.1.-) (TM0488) from Thermotoga maritima at 2.80 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NV8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP7.52935.0% MPD, 10.0% PEG-6000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8556.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.973α = 90
b = 58.611β = 109.46
c = 85.667γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2003-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

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
12.836.09960.06413.33.41582874.56
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)
12.82.8773.30.4631.72.4884

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 REPLACEMENTTHROUGHOUT1nv82.836.091502480195.940.211560.208240.27281RANDOM85.35
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]
5.5-1.54-7.50.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.817
r_dihedral_angle_3_deg17.375
r_dihedral_angle_4_deg16.09
r_dihedral_angle_1_deg7.197
r_scangle_it4.495
r_scbond_it3.285
r_angle_refined_deg1.507
r_mcangle_it1.394
r_mcbond_it0.995
r_angle_other_deg0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.817
r_dihedral_angle_3_deg17.375
r_dihedral_angle_4_deg16.09
r_dihedral_angle_1_deg7.197
r_scangle_it4.495
r_scbond_it3.285
r_angle_refined_deg1.507
r_mcangle_it1.394
r_mcbond_it0.995
r_angle_other_deg0.78
r_mcbond_other0.383
r_symmetry_hbond_refined0.352
r_symmetry_vdw_refined0.232
r_nbd_refined0.23
r_symmetry_vdw_other0.22
r_nbd_other0.194
r_nbtor_refined0.193
r_xyhbond_nbd_refined0.183
r_nbtor_other0.089
r_chiral_restr0.071
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4116
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms54

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
CCP4data scaling