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Crystal structure of the transmembrane domain and linker region of Salpingoeca rosetta rhodopsin phosphodiesterase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5 293 25% (w/v) PEG 500DME, 100mM Na-citrate, pH 5.0, 100mM NaK-tartrate
Crystal Properties Matthews coefficient Solvent content 3.42 64.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.3 α = 90 b = 136.53 β = 90 c = 206.54 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2019-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 3.5 49.4 98.1 0.673 0.934 3.9 6.55 13712 49.61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.71 2.868 0.393
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7CJ3 3.5 49.4 1.34 13675 687 97.75 0.2686 0.2663 0.2695 0.3144 0.3181 33.37
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 f_dihedral_angle_d 13.4668 f_angle_d 0.6351 f_chiral_restr 0.0358 f_plane_restr 0.0032 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4485 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 126
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing