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Crystal Structure of a putative sarcosine dimethylglycine methyltransferase from Galdieria sulphuraria
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M Bis Tris pH 7.0) mixed in a 1:1 ratio with the Well Solution (23% MEPEG 5K, 0.03 M sarcosine, 0.1 M MOPS pH 7.0), Cryoprotected with: well solution supplemented with up to 15% glycerol, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.541 α = 90 b = 291.433 β = 90 c = 86.34 γ = 90
Symmetry Space Group C 2 2 21
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 MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2006-11-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97923, 0.96400 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.95 50 99.4 0.11 7.618 7.2 89709
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2.02 95 0.597 1.775 5.1 8471
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.946 48.771 89679 4502 99.242 0.168 0.166 0.193 0.221 0.2376 RANDOM 21.559
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] 0.295 -0.701 0.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.257 r_dihedral_angle_4_deg 19.467 r_dihedral_angle_3_deg 13.913 r_dihedral_angle_1_deg 6.026 r_scangle_it 3.445 r_scbond_it 2.305 r_angle_refined_deg 1.452 r_mcangle_it 1.352 r_mcbond_it 0.848 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.257 r_dihedral_angle_4_deg 19.467 r_dihedral_angle_3_deg 13.913 r_dihedral_angle_1_deg 6.026 r_scangle_it 3.445 r_scbond_it 2.305 r_angle_refined_deg 1.452 r_mcangle_it 1.352 r_mcbond_it 0.848 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.141 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8744 Nucleic Acid Atoms Solvent Atoms 1042 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction