☰ Navigation Tabs
Crystal structure of the mouse C5a-desArg anaphylatoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.3 277 0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate
Crystal Properties Matthews coefficient Solvent content 2.52 51.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.21 α = 90 b = 55.21 β = 90 c = 117.43 γ = 90
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 2013-11-13 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.1 50 99.9 0.113 0.123 14.62 6.4 20489 2 -3 23.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 100 0.662 0.722 2.95 6.4
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 4P3A 2.1 32.509 2 20350 1044 99.26 0.1825 0.1803 0.1827 0.2241 0.225 random 35.78
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 13.645 f_angle_d 0.711 f_chiral_restr 0.029 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2212 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 45
Software Software Software Name Purpose XDS data scaling XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing PHENIX refinement