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Room temperature structure of bacteriorhodopsin from lipidic cubic phase obtained with serial millisecond crystallography using synchrotron radiation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H68
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5.6 294 Precipitant: 27%-39% PEG 2000, 100 mM phosphate buffer pH 5.6.
MAG 9.9 used for LCP formation.
Crystallization setup in Hamilton syringe with tube of LCP surrounded by precipitant.
Crystal Properties Matthews coefficient Solvent content 2.49 50.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.79 α = 90 b = 62.79 β = 90 c = 109.67 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 294 CCD RAYONIX MX-225 2014-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 1.0 ESRF ID13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 36.56 100 0.224 3.57 127 9655 9655
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 2.4 2.46 100 1.16 88.8
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 1H68 2.4 31.4 9633 441 99.96 0.2072 0.2053 0.2133 0.249 0.2479 RANDOM 58.52
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] 2.28 1.14 2.28 -7.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.914 r_dihedral_angle_4_deg 15.673 r_dihedral_angle_3_deg 14.77 r_dihedral_angle_1_deg 4.54 r_mcangle_it 2.673 r_mcbond_it 1.485 r_mcbond_other 1.483 r_angle_refined_deg 1.013 r_angle_other_deg 0.749 r_chiral_restr 0.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.914 r_dihedral_angle_4_deg 15.673 r_dihedral_angle_3_deg 14.77 r_dihedral_angle_1_deg 4.54 r_mcangle_it 2.673 r_mcbond_it 1.485 r_mcbond_other 1.483 r_angle_refined_deg 1.013 r_angle_other_deg 0.749 r_chiral_restr 0.052 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1756 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement PHASER phasing PDB_EXTRACT data extraction