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Crystal structure of YnaF (Universal Stress Protein F) from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FH0 PDB ID 3FH0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Under oil, Microbatch 8.5 298 30% PEG 4000, 100mM Tris-HCl pH 8.5, 200mM Magnesium chloride, 100mM guanidine hydrochloride, Under oil, Microbatch, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.08 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.76 α = 90 b = 132.76 β = 90 c = 32.71 γ = 90
Symmetry Space Group P 43 21 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 MARMOSAIC 225 mm CCD bent collimating mirror and toroid 2011-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.953720 ESRF BM14
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 1 1.8 33.19 99.9 0.075 10.2 27850 21.9
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) 1 1.8 1.9 99.9 0.675 3.4 9.5 3980
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ID 3FH0 1.8 33.19 26406 1397 99.91 0.19133 0.18913 0.198 0.23471 0.2428 RANDOM 36.983
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] -0.43 -0.43 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.76 r_dihedral_angle_4_deg 14.733 r_dihedral_angle_3_deg 12.619 r_long_range_B_refined 6.834 r_long_range_B_other 6.833 r_dihedral_angle_1_deg 5.908 r_scangle_other 2.649 r_mcangle_it 2.263 r_mcangle_other 2.263 r_angle_refined_deg 1.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.76 r_dihedral_angle_4_deg 14.733 r_dihedral_angle_3_deg 12.619 r_long_range_B_refined 6.834 r_long_range_B_other 6.833 r_dihedral_angle_1_deg 5.908 r_scangle_other 2.649 r_mcangle_it 2.263 r_mcangle_other 2.263 r_angle_refined_deg 1.915 r_scbond_it 1.73 r_scbond_other 1.729 r_mcbond_it 1.366 r_mcbond_other 1.366 r_angle_other_deg 0.927 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2065 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 78
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling