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Mechanistic insights from the crystal structure of an inward proton-transporting Anabaena sensory rhodopsin mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XIO PDB entry 1XIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5.6 293 MPD, pH 5.6, magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.08 60.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.265 α = 90 b = 104.301 β = 90 c = 111.386 γ = 90
Symmetry Space Group P 21 21 21
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 2013-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 33.19 96.7 11.4 1.93 28486
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 98.7 2
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 1XIO 2.3 33.19 26889 1449 96.59 0.22137 0.21976 0.219 0.24951 0.2503 RANDOM 20.739
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.234 r_dihedral_angle_4_deg 19.81 r_dihedral_angle_3_deg 13.909 r_long_range_B_refined 5.606 r_dihedral_angle_1_deg 4.736 r_mcangle_it 1.709 r_scbond_it 1.365 r_angle_refined_deg 1.203 r_mcbond_it 1.033 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.234 r_dihedral_angle_4_deg 19.81 r_dihedral_angle_3_deg 13.909 r_long_range_B_refined 5.606 r_dihedral_angle_1_deg 4.736 r_mcangle_it 1.709 r_scbond_it 1.365 r_angle_refined_deg 1.203 r_mcbond_it 1.033 r_chiral_restr 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3556 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 475
Software Software Software Name Purpose REFMAC refinement