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Crystal structure of the batho intermediate of squid rhodopsin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z73 PDB ENTRY 2Z73
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 277 3.2M ammonium sulfate, 20mM MES, 75mM EDTA, 10mM beta-mercaptoethanol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.43 64.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.36 α = 90 b = 122.36 β = 90 c = 158.22 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 MAR CCD 165 mm 2009-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW14A 1.0 Photon Factory AR-NW14A
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 2.8 88 95.5 0.078 11.2 3.3 31468 3 44.7
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 2.8 2.95 95 0.529 2 2.8 4562
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-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 2Z73 2.8 15 33086 22229 1080 67.7 0.2953 0.3007 0.3448 0.2936 RANDOM 58.7828
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] -10.272 -14.469 -10.272 20.545
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 4.1 c_mcangle_it 3.048 c_scbond_it 2.639 c_mcbond_it 1.821
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5542 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 141
Software Software Software Name Purpose MAR345 data collection CNS refinement MOSFLM data reduction SCALA data scaling CNS phasing