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Structure of marine actinobacteria clade rhodopsin (MacR) in orange form in P1211 space group
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 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.688 α = 90 b = 102.009 β = 99.75 c = 56.601 γ = 90
Symmetry Space Group P 1 21 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 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 1.7 48.94 98 0.083 0.086 0.022 1 25.5 14.5 48957
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 1.7 1.73 97.3 1.765 1.829 0.474 0.71 14.5
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 1.7 48.94 46448 2481 97.85 0.1987 0.1974 0.2074 0.2219 0.2301 RANDOM 28.564
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] -0.19 0.31 0.79 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.465 r_dihedral_angle_4_deg 20.474 r_dihedral_angle_3_deg 15.461 r_dihedral_angle_1_deg 4.291 r_angle_other_deg 1.457 r_angle_refined_deg 1.22 r_chiral_restr 0.063 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.465 r_dihedral_angle_4_deg 20.474 r_dihedral_angle_3_deg 15.461 r_dihedral_angle_1_deg 4.291 r_angle_other_deg 1.457 r_angle_refined_deg 1.22 r_chiral_restr 0.063 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3360 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 283
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing