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Crystal structure the GYF domain of S. Cerevisiae SMY2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FMA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 18% polyacrylic acid, 0.15M MgCl2, 0.1M Na-HEPES, pH 7.5, Vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.38 63.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.4 α = 90 b = 68.4 β = 90 c = 111.321 γ = 120
Symmetry Space Group P 65 2 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 CCD MAR CCD 165 mm 2006-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 1.8 25.19 99.8 0.075 31.4 20.9 14884 14884 25.5
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 1.8 1.9 99.7 0.656 5.2 20.2 2107
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3FMA 1.8 25.19 14837 14837 747 99.64 0.208 0.2223 0.224 0.2378 RANDOM 15.654
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] -0.29 -0.14 -0.29 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.984 r_dihedral_angle_4_deg 17.912 r_dihedral_angle_3_deg 12.324 r_dihedral_angle_1_deg 5.427 r_scangle_it 3.415 r_scbond_it 2.366 r_mcangle_it 2.304 r_mcbond_it 1.51 r_angle_refined_deg 1.497 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.984 r_dihedral_angle_4_deg 17.912 r_dihedral_angle_3_deg 12.324 r_dihedral_angle_1_deg 5.427 r_scangle_it 3.415 r_scbond_it 2.366 r_mcangle_it 2.304 r_mcbond_it 1.51 r_angle_refined_deg 1.497 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 639 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction