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Crystal Structure of Mouse Glycine N-Methyltransferase (Tetragonal Form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XVA PDB entry 1XVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 298 PEG4000, isopropanol, Tris, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.55 51.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.7 α = 90 b = 70.7 β = 90 c = 266.03 γ = 90
Symmetry Space Group P 41 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 103 IMAGE PLATE MARRESEARCH mirrors 2002-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS 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 2.95 30 99.7 0.068 6.7 3.7 14973
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 2.95 3.05 99.7 0.431 1.8 3.9
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 1XVA 2.95 10.5 14973 13784 823 99.77 0.21048 0.21048 0.20678 0.27266 RANDOM 27.202
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] 1.67 1.67 -3.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.264 r_scangle_it 3.218 r_angle_refined_deg 2.167 r_scbond_it 2.08 r_mcangle_it 1.308 r_mcbond_it 0.694 r_symmetry_vdw_refined 0.308 r_nbd_refined 0.255 r_symmetry_hbond_refined 0.193 r_xyhbond_nbd_refined 0.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.264 r_scangle_it 3.218 r_angle_refined_deg 2.167 r_scbond_it 2.08 r_mcangle_it 1.308 r_mcbond_it 0.694 r_symmetry_vdw_refined 0.308 r_nbd_refined 0.255 r_symmetry_hbond_refined 0.193 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.134 r_bond_refined_d 0.024 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4356 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement MAR345 data collection CCP4 data scaling CNS phasing