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Crystal structure of a rhodopsin stabilizing mutant expressed in mammalian cells
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GZM PDB ENTRY 1GZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 VAPOUR DIFFUSION IN SITTING DROPS OF 10-15 MG/ML PROTEIN AND 0.2% C8E4,0.05%LDAO AGAINST 1.1-1.7M LITHIUM SULFATE, 0.1M HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 3.64 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.3 α = 90 b = 109.3 β = 90 c = 77.7 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 100 CCD MARRESEARCH MICROFOCUSING 2004-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 ESRF ID13
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 3.4 50 95.9 0.24 5.42 3.03 13689 -3 58.2
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 3.4 3.5 84.8 0.7 1.79 2.79
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 ENTRY 1GZM 3.4 50 13689 407 95.9 0.2896 0.2896 0.2622 0.3299 0.2853 0.325 55.6579
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] -3.497 -7.211 -3.497 6.994
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.40625 c_scangle_it 3.81 c_mcangle_it 3.13 c_scbond_it 2.39 c_mcbond_it 1.78 c_angle_deg 1.66 c_improper_angle_d 1.11414 c_bond_d 0.014 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.40625 c_scangle_it 3.81 c_mcangle_it 3.13 c_scbond_it 2.39 c_mcbond_it 1.78 c_angle_deg 1.66 c_improper_angle_d 1.11414 c_bond_d 0.014 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5184 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 68
Software Software Software Name Purpose CNS refinement XDS data reduction XSCALE data scaling MOLREP phasing