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Crystal Structure of Human Glycine N-Methyltransferase
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 5.6 273 PEG4000, Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.77 55.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.84 α = 90 b = 83.23 β = 90 c = 114.88 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 1 103 IMAGE PLATE MARRESEARCH mirrors 2002-04-02 2 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 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 2 2.55 12 98.3 0.051 9.9 3.7 23864 23864
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) 2 2.55 2.69 98.3 0.389 1.8 3.6
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 2.55 12 23864 22070 1623 98.37 0.2249 0.22492 0.2218 0.26605 RANDOM 29.659
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] -0.13 0.48 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.843 r_scangle_it 4.003 r_scbond_it 2.588 r_angle_refined_deg 2.167 r_angle_other_deg 1.605 r_mcangle_it 1.568 r_mcbond_it 0.862 r_symmetry_hbond_refined 0.438 r_symmetry_vdw_other 0.345 r_nbd_other 0.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.843 r_scangle_it 4.003 r_scbond_it 2.588 r_angle_refined_deg 2.167 r_angle_other_deg 1.605 r_mcangle_it 1.568 r_mcbond_it 0.862 r_symmetry_hbond_refined 0.438 r_symmetry_vdw_other 0.345 r_nbd_other 0.252 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.133 r_symmetry_vdw_refined 0.119 r_nbtor_other 0.1 r_gen_planes_other 0.033 r_bond_refined_d 0.027 r_gen_planes_refined 0.017 r_bond_other_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4240 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MAR345 data collection CCP4 data scaling CNS phasing