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Crystal structure of N5-glutamine methyltransferase, HemK(EC 2.1.1.-) (TM0488) from Thermotoga maritima at 2.80 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NV8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 7.5 293 5.0% MPD, 10.0% PEG-6000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.85 56.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.973 α = 90 b = 58.611 β = 109.46 c = 85.667 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC 2003-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 36.09 96 0.064 13.3 3.4 15828 74.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 73.3 0.463 1.7 2.4 884
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1nv8 2.8 36.09 15024 801 95.94 0.21156 0.20824 0.2118 0.27281 0.2723 RANDOM 85.35
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 -7.5 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.817 r_dihedral_angle_3_deg 17.375 r_dihedral_angle_4_deg 16.09 r_dihedral_angle_1_deg 7.197 r_scangle_it 4.495 r_scbond_it 3.285 r_angle_refined_deg 1.507 r_mcangle_it 1.394 r_mcbond_it 0.995 r_angle_other_deg 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.817 r_dihedral_angle_3_deg 17.375 r_dihedral_angle_4_deg 16.09 r_dihedral_angle_1_deg 7.197 r_scangle_it 4.495 r_scbond_it 3.285 r_angle_refined_deg 1.507 r_mcangle_it 1.394 r_mcbond_it 0.995 r_angle_other_deg 0.78 r_mcbond_other 0.383 r_symmetry_hbond_refined 0.352 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.23 r_symmetry_vdw_other 0.22 r_nbd_other 0.194 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.183 r_nbtor_other 0.089 r_chiral_restr 0.071 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4116 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 54
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling