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Bacterioruberin in the trimeric structure of archaerhodopsin-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EI4 PDB ENTRY 2EI4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 288 2.9M ammonium sulfate, 3.25mg/ml nonyl glucoside, 0.16M NaCl, 8% trehalose, 0.04% Na-azide, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 3.45 64.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.83 α = 90 b = 108.83 β = 90 c = 220.71 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 CCD ADSC QUANTUM 210 mirrors 2006-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0 SPring-8 BL44B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 54 100 0.086 0.081 22.5 8.6 51050 51050 43.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 100 0.42 0.42 5.1 8.7 7441
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 2EI4 2.5 15 50784 47521 4865 93.6 0.201 0.201 0.2033 0.232 0.2326 random 42.78
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] -0.158 -1.073 -0.158 0.316
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 17.74 c_angle_deg 1.322 c_improper_angle_d 0.582 c_bond_d 0.00797
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7374 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 612
Software Software Software Name Purpose ADSC data collection MOLREP phasing CNS refinement MOSFLM data reduction SCALA data scaling