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Crystal structure of squid rhodopsin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GZM PDB ENTRY 1GZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 277 3M ammonium sulfate, 30mM MES, 30mM EDTA, 10mM beta-mercaptoethanol, pH6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.45 64.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.55 α = 90 b = 122.55 β = 90 c = 158.74 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 90 CCD RIGAKU JUPITER 210 2007-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 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 2.5 57 99.2 0.068 0.068 14.7 3.9 46274
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) 2.5 2.64 0.677 0.495 1.8 3.8 6771
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 PDB ENTRY 1GZM 2.5 15 43279 2161 92.2 0.188 0.188 0.1859 0.206 0.2048 RANDOM 60.77
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] -0.144 -1.1 -0.144 0.288
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.3 c_scangle_it 3.17 c_mcangle_it 2.66 c_scbond_it 2.41 c_mcbond_it 1.66 c_angle_deg 1.18 c_improper_angle_d 0.84 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.3 c_scangle_it 3.17 c_mcangle_it 2.66 c_scbond_it 2.41 c_mcbond_it 1.66 c_angle_deg 1.18 c_improper_angle_d 0.84 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5542 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 236
Software Software Software Name Purpose ADSC data collection MOLREP phasing CNS refinement MOSFLM data reduction SCALA data scaling