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Crystal structure of the COP9 signalosome, a P1 crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D10 4d10 chains A-H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 273 CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Crystal Properties Matthews coefficient Solvent content 3.73 67.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.638 α = 92.34 b = 150.983 β = 92.62 c = 336.72 γ = 119.88
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 2011-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0004 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 5.5 49.64 94.9 0.072 0.065 0.997 5.4 1.9 79098
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 5.5 5.61 88.7 1.329 1.205 0.166 0.6 1.9 4292
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 4d10 chains A-H 5.5 49.64 78769 1996 96.92 0.2548 0.2542 0.2928 0.2821 0.3255 RANDOM 125.221
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] 7.74 3.59 -3.95 7.98 -5.52 -22.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.218 r_dihedral_angle_3_deg 15.272 r_dihedral_angle_4_deg 13.045 r_dihedral_angle_1_deg 5.567 r_angle_refined_deg 0.839 r_angle_other_deg 0.745 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.218 r_dihedral_angle_3_deg 15.272 r_dihedral_angle_4_deg 13.045 r_dihedral_angle_1_deg 5.567 r_angle_refined_deg 0.839 r_angle_other_deg 0.745 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 124422 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose Aimless data scaling XDS data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction