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Structural characterization of a blue chromoprotein and its yellow mutant from the sea anemone cnidopus japonicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IB5 PDB ENTRY 2IB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.2M NaH2PO4, 20mM Tris-HCl, 150mM NaCl, 20% PEG3350, 20% glycerol, 2mM TCEP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.15 42.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.079 α = 90 b = 126.926 β = 101.97 c = 100.084 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 CCD Bruker Platinum 135 Helios Multilayer Graded X-ray Optics 2005-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 50 100 0.062 39.65 8.6 121926 121926 16.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 88.5 4.1 10246
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 2IB5 2 50 113671 113671 5761 80.3 0.198 0.198 0.1905 0.244 0.2343 random 16.2
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 c_dihedral_angle_d 26.4 c_scangle_it 3.154 c_scbond_it 2.294 c_mcangle_it 1.748 c_angle_deg 1.644 c_mcbond_it 1.196 c_improper_angle_d 0.68 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14352 Nucleic Acid Atoms Solvent Atoms 1340 Heterogen Atoms 80
Software Software Software Name Purpose PROTEUM PLUS data collection CNS refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling CNS phasing