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Crystal Structure of a Member of YjgF Family from Sulfolobus Tokodaii (ST0811)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QD9 PDB ENTRY 1QD9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 293 PEG 10000, Bis-Tris, ammonium acetate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.98 α = 90 b = 54.98 β = 90 c = 221.557 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS VII 2004-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
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 22.051 99.8 0.061 0.055 9.8 6.2 16882 16882 5.1 17.336
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 2.11 99.8 0.151 0.137 5.1 5.9 182
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QD9 2 19.03 16877 16877 852 99.82 0.14787 0.14787 0.14578 0.1495 0.18799 0.1887 RANDOM 18.36
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] 0.27 0.14 0.27 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.343 r_scangle_it 4.987 r_scbond_it 3.028 r_mcangle_it 1.79 r_angle_refined_deg 1.488 r_mcbond_it 1.005 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.343 r_scangle_it 4.987 r_scbond_it 3.028 r_mcangle_it 1.79 r_angle_refined_deg 1.488 r_mcbond_it 1.005 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.12 r_chiral_restr 0.114 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1979 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CCP4 data scaling MOLREP phasing