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Crystal Structure Analysis of the Bacteriorhodopsin in Facial Amphiphile-7 DMPC Bicelle
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KME PDB ENTRY 1KME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.4 300.15 3.6M Sodium Phosphate (pH 3.4), 3.5% Triethyleneglycol, 180mM Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 300.15K
Crystal Properties Matthews coefficient Solvent content 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.16 α = 90 b = 113.29 β = 114.27 c = 56.19 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 CCD ADSC QUANTUM 315 2011-04-15 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) 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 2 46.67 96.6 0.074 6.5 2.1 35395 34192
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 2 2.11 95.1 0.55 1.7 2.1 5132
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1KME 2 42.08 35395 33257 1667 98.29 0.15942 0.15942 0.15875 0.1626 0.17183 0.1802 RANDOM 28.373
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.693 r_dihedral_angle_4_deg 15.504 r_dihedral_angle_3_deg 14.49 r_dihedral_angle_1_deg 4.877 r_angle_refined_deg 1.879 r_angle_other_deg 1.317 r_chiral_restr 0.151 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.693 r_dihedral_angle_4_deg 15.504 r_dihedral_angle_3_deg 14.49 r_dihedral_angle_1_deg 4.877 r_angle_refined_deg 1.879 r_angle_other_deg 1.317 r_chiral_restr 0.151 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.007 r_gen_planes_other 0.006 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_it r_mcbond_other r_mcangle_it r_scbond_it 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 3512 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 91
Software Software Software Name Purpose Blu-Ice data collection PHASES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling