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Crystal structure of complement C4b re-refined using iMDFF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 the crystals appeared after mixing C4b at 4 mg/ml in 20 mM HEPES pH 7.5, 100 mM sodium chloride with 100 mM HEPES pH 7.0, 400 mM magnesium chloride, 7.5% PEG8000 and a microseeding stock at the volume ration 1:1:0.5. The crystals appeared in 1-2 weeks and reached the final size in 1 month
Crystal Properties Matthews coefficient Solvent content 3.41 63.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.5 α = 90 b = 161.08 β = 107.26 c = 131.6 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 PILATUS 6M-F 2014-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9840 ESRF ID23-1
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 3.5 49.54 98.6 0.492 0.949 4.55 7.14 60261 -3 101.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.59 99.3 3.133 0.65
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4xam 3.5 49.376 1.33 60234 2014 98.67 0.2495 0.248 0.2485 0.2935 0.2957 122.3647
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 14.347 f_angle_d 0.826 f_chiral_restr 0.047 f_plane_restr 0.009 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 24256 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing