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Crystal structure of trigonal crystal form of ground-state rhodopsin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HZX PDB entry 1HZX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.3 278 80 mM MES, pH 6.3, 110 mM N-nonyl-beta-D-glucoside, 200 mM zinc acetate, 0.1% sodium azide, 16 mM beta-mercaptoethanol, 2.6% Merpol HCS,
equilibrated against 3.1-3.3 M ammonium sulfate, VAPOR DIFFUSION, temperature 278K
Crystal Properties Matthews coefficient Solvent content 4.5 72.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.866 α = 90 b = 159.866 β = 90 c = 142.15 γ = 120
Symmetry Space Group P 31 1 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 315 2004-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97970 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 4 50 99.7 0.087 21.1 10.6 17705 17705 185
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 4 4.15 100
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 1HZX 4.1 30 16375 16375 832 99.82 0.38367 0.38367 0.38229 0.384 0.41153 0.4119 RANDOM 185
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] -13.16 -6.58 -13.16 19.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.202 r_dihedral_angle_3_deg 21.531 r_dihedral_angle_4_deg 17.059 r_dihedral_angle_1_deg 6.376 r_angle_refined_deg 1.327 r_symmetry_vdw_refined 0.342 r_nbtor_refined 0.316 r_nbd_refined 0.23 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.202 r_dihedral_angle_3_deg 21.531 r_dihedral_angle_4_deg 17.059 r_dihedral_angle_1_deg 6.376 r_angle_refined_deg 1.327 r_symmetry_vdw_refined 0.342 r_nbtor_refined 0.316 r_nbd_refined 0.23 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 7665 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 218
Software Software Software Name Purpose REFMAC refinement SSRL data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing