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Structure of Caulobacter crescentus Suppressor of copper sensitivity protein C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XVW chain A residues 50-224
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.25 277.15 Protein reduced with DTT and purified in 25 mM HEPES pH 7.5, 150 mM NaCl. Protein concentrated to 130 mg/ml. 1ul of protein solution mixed with 1ul of crystallant solution:
39% MPD, 200 mM NaAcetate, 20 mM CaCl2 pH 7.25
Crystal Properties Matthews coefficient Solvent content 3.51 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.948 α = 90 b = 113.948 β = 90 c = 48.695 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 PIXEL DECTRIS EIGER X 16M 2021-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9536 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.63 49.34 98.75 0.052 0.054 0.016 1 22.51 12 10854 90.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.63 2.74 94.76 1.46 1.52 0.431 0.961 1.85 12.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4VXW res 50-224 chain A 2.63 49.34 1.36 10766 1081 98.73 0.2263 0.2237 0.2228 0.2502 0.2485 random selection 122.3
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 12.2412 f_angle_d 0.4463 f_chiral_restr 0.038 f_plane_restr 0.0036 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1667 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing