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Structural Proteomics From Crude Native Rod Outer Segments
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B6R pdb entry 3B6R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 277 1.8 M ammonium sulfate, 0.1 M HEPES, 3% PEG 1K, pH 7.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.88 57.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.976 α = 90 b = 95.976 β = 90 c = 107.09 γ = 90
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 2013-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.07500 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.65 42.922 99.9 0.087 0.087 45.4 6.2 116751 116751
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 99.6 0.074 0.074 2.8 5.9
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 (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 3B6R 1.65 42.922 116751 109588 5779 98.63 0.22275 0.22153 0.233 0.24575 0.2539 RANDOM 26.493
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] 0.19 0.19 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.6 r_dihedral_angle_4_deg 21.416 r_dihedral_angle_3_deg 14.24 r_dihedral_angle_1_deg 6.793 r_long_range_B_refined 5.791 r_long_range_B_other 5.785 r_scangle_other 4.846 r_scbond_it 3.353 r_scbond_other 3.352 r_mcangle_it 3.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.6 r_dihedral_angle_4_deg 21.416 r_dihedral_angle_3_deg 14.24 r_dihedral_angle_1_deg 6.793 r_long_range_B_refined 5.791 r_long_range_B_other 5.785 r_scangle_other 4.846 r_scbond_it 3.353 r_scbond_other 3.352 r_mcangle_it 3.056 r_mcangle_other 3.056 r_mcbond_it 2.243 r_mcbond_other 2.243 r_angle_refined_deg 1.966 r_angle_other_deg 0.927 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5808 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 5
Software Software Software Name Purpose ADSC data collection MLPHARE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling