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Crystal Structure of Escherichia coli-Expressed Halobacterium salinarum Bacteriorhodopsin in the Trimeric Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 The crystals were grown using in meso crystallization technique
Crystal Properties Matthews coefficient Solvent content 2.04 39.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.84 α = 90 b = 60.76 β = 99.78 c = 113.36 γ = 90
Symmetry Space Group C 1 2 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 PSI PILATUS 6M 2013-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 49.2 98.8 0.071 13.7 4.5 56113
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 98.3 1.102 1.41 4.5
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 1C3W 1.9 49.2 52689 2770 98.83 0.18502 0.18345 0.196 0.2139 0.2228 RANDOM 33.762
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] 0.79 0.01 -1.03 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.323 r_dihedral_angle_3_deg 14.017 r_dihedral_angle_4_deg 13.98 r_long_range_B_refined 7.71 r_long_range_B_other 7.71 r_scangle_other 6.235 r_mcangle_other 4.557 r_scbond_it 4.557 r_scbond_other 4.556 r_mcangle_it 4.554
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.323 r_dihedral_angle_3_deg 14.017 r_dihedral_angle_4_deg 13.98 r_long_range_B_refined 7.71 r_long_range_B_other 7.71 r_scangle_other 6.235 r_mcangle_other 4.557 r_scbond_it 4.557 r_scbond_other 4.556 r_mcangle_it 4.554 r_dihedral_angle_1_deg 3.949 r_mcbond_other 3.529 r_mcbond_it 3.528 r_angle_other_deg 1.327 r_angle_refined_deg 0.938 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5279 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 320
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing