☰ Navigation Tabs
Bacterial protein - dp_3-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9HWH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298.15 7-8 % (W/v) PEG 4000, 100 mM HEPES pH 7.2, 100 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.71 54.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.71 α = 90 b = 99.356 β = 106.06 c = 103.063 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2021-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 1.0 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 44.32 99.38 0.06389 0.999 18.75 7.1 116716
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.071 1.003 0.837
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 44.32 1.35 116583 1816 99.4 0.185 0.1843 0.1856 0.2321 0.234 45.38
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.6388 f_angle_d 0.8743 f_chiral_restr 0.0548 f_plane_restr 0.0116 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11002 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 167
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASES phasing