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Crystal structure of thermophilic SlyD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D6O PDB ENTRY 1D6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 286 60mg/ml protein, 1:1 mixing, 2M Ammonium sulfate, 2% PEG 400, 1% Thiocyanate, 100mM HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Crystal Properties Matthews coefficient Solvent content 4.69 73.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.78 α = 90 b = 121.78 β = 90 c = 76.26 γ = 120
Symmetry Space Group P 63 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 180 CCD MARMOSAIC 225 mm CCD mirrors 2007-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.41 30 96.6 0.093 0.107 21.98 13.1 13374 12921 -3 43.405
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.55 92.9 0.582 0.45 4.4 11.32 1885
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 MR THROUGHOUT PDB ENTRY 1D6O 2.41 28.27 -3 13374 11955 969 96.6 0.19 0.187 0.191 0.226 0.1978 RANDOM 44.556
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 -0.06 -0.13 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.398 r_dihedral_angle_4_deg 17.68 r_dihedral_angle_3_deg 16.948 r_dihedral_angle_1_deg 5.994 r_scangle_it 2.189 r_mcangle_it 2.187 r_angle_refined_deg 1.62 r_scbond_it 1.409 r_mcbond_it 1.253 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.398 r_dihedral_angle_4_deg 17.68 r_dihedral_angle_3_deg 16.948 r_dihedral_angle_1_deg 5.994 r_scangle_it 2.189 r_mcangle_it 2.187 r_angle_refined_deg 1.62 r_scbond_it 1.409 r_mcbond_it 1.253 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1217 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 31
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction PHASER phasing