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Crystal structure of marine actinobacteria clade rhodopsin (MAR) in the M-like state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 1.0 M NH4SO4, 0.1 M NaOAc pH 5.2
Crystal Properties Matthews coefficient Solvent content 2.36 47.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.686 α = 63.66 b = 56.628 β = 78.98 c = 57.386 γ = 80.33
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 PILATUS 6M-F 2015-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97241 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.6 50.98 99.7 0.054 0.057 0.017 1 23.2 10.9 59048
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 99.7 0.892 0.937 0.284 0.772 10.6
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 5JSI 1.6 50.57 56027 3019 99.7 0.1769 0.1754 0.1861 0.2044 0.216 RANDOM 27.59
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] -0.1 0.04 -0.41 -0.56 -0.11 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.267 r_dihedral_angle_4_deg 22.212 r_dihedral_angle_3_deg 16.229 r_dihedral_angle_1_deg 4.148 r_angle_other_deg 1.431 r_angle_refined_deg 1.312 r_chiral_restr 0.067 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.267 r_dihedral_angle_4_deg 22.212 r_dihedral_angle_3_deg 16.229 r_dihedral_angle_1_deg 4.148 r_angle_other_deg 1.431 r_angle_refined_deg 1.312 r_chiral_restr 0.067 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3365 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 335
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing