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Crystal structure of an anion-free yellow form of pharaonis halorhodopsin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A7K PDB ENTRY 3A7K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 288 Crystallization: 3.5 mg/ml halorhodopsin, 5mg/ml nonylglucoside, 2.8M ammonium sulfate, 0.1 M glycine, 0.1M NaCl Post-crystallization soaking: 3 M ammonium sulfate, 0.2 M glycine (pH10.0), 30% trehalose
, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 3.19 61.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.96 α = 90 b = 97.97 β = 128.68 c = 100.65 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 315 mirrors 2010-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 2.1 48.9 99.2 0.102 0.102 9.5 3.2 67957 67414 23.3
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 2.1 2.21 99.2 0.54 0.54 1.4 3.2 9782
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 3A7K 2.1 15 67894 67243 3429 99 0.235 0.235 0.2321 0.266 0.2632 RANDOM 29.183
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] 1.653 -0.322 4.528 -6.181
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.41146 c_scangle_it 2.42 c_mcangle_it 1.83 c_scbond_it 1.816 c_mcbond_it 1.228 c_angle_d 1.10697 c_improper_angle_d 0.78623 c_bond_d 0.006297
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5897 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 198
Software Software Software Name Purpose ADSC data collection CNS refinement MOSFLM data reduction SCALA data scaling CNS phasing