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Crystal structure of a blue-light absorbing proteorhodopsin double-mutant D97N/Q105L from HOT75
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KLY PDB ID: 4KLY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 20 mg/mL protein mixed with equal volume of reservoir solution (0.2 M ammonium acetate, 0.1 M bis-tris pH 6.5, 45%(v/v) MPD), VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.19 61.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.4 α = 90 b = 168.9 β = 90 c = 65.7 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2011-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U
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 2.6 20 98.5 0.105 11.28 7.06 48405
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 2.6 2.97 98.6 1.12 1.76 7.08 11088
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 ID: 4KLY 2.6 19.95 52622 2819 98.71 0.22173 0.21925 0.2178 0.26654 0.2655 RANDOM 72.695
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] -0.05 0.03 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.031 r_dihedral_angle_3_deg 17.924 r_dihedral_angle_1_deg 5.205 r_dihedral_angle_4_deg 4.296 r_angle_refined_deg 1.595 r_chiral_restr 0.178 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.031 r_dihedral_angle_3_deg 17.924 r_dihedral_angle_1_deg 5.205 r_dihedral_angle_4_deg 4.296 r_angle_refined_deg 1.595 r_chiral_restr 0.178 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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_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 8747 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 100
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XDS data scaling