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Crystal structure of H176N mutant of human Glycine N-Methyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R74 pdb entry 1R74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.8 289 10% PEG4000, 0.1M Na citrate, 5% glycerol, pH 5.8, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.79 55.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.116 α = 90 b = 83.279 β = 90 c = 115.45 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH mirrors 2002-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR571 1.5418
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 2.65 20 96.2 0.058 28.6 4.5 21138 21138 -3
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 2.65 2.74 93.5 0.379 4.5 4.1 2015
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1R74 2.7 13 18950 18950 1369 98.9 0.23918 0.23918 0.23599 0.28172 RANDOM 26.855
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] 0.22 0.63 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.86 r_scangle_it 2.545 r_angle_refined_deg 2.001 r_scbond_it 1.941 r_mcangle_it 1.061 r_mcbond_it 0.592 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.241 r_chiral_restr 0.134 r_xyhbond_nbd_refined 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.86 r_scangle_it 2.545 r_angle_refined_deg 2.001 r_scbond_it 1.941 r_mcangle_it 1.061 r_mcbond_it 0.592 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.241 r_chiral_restr 0.134 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4268 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing