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Crystal structure of octopus S-crystallin Q108F mutant in complex with glutathione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other simulated model for S-crystallin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 295 0.5% PEG8000, 0.1 M HEPES, 1.65 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.15 42.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.322 α = 90 b = 114.322 β = 90 c = 63.927 γ = 120
Symmetry Space Group P 64 2 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 CCD ADSC QUANTUM 315r 2011-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.976 NSRRC BL13C1
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 2.35 30 99.9 0.164 13.3 7.1 10705
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 2.35 2.43 100 0.532 4 7.2
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 simulated model for S-crystallin 2.35 30 10177 512 99.83 0.19517 0.1924 0.1919 0.24992 0.2487 RANDOM 24.753
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] -0.48 -0.24 -0.48 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.832 r_dihedral_angle_3_deg 17.901 r_dihedral_angle_4_deg 16.037 r_dihedral_angle_1_deg 5.728 r_angle_refined_deg 1.272 r_chiral_restr 0.099 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.832 r_dihedral_angle_3_deg 17.901 r_dihedral_angle_4_deg 16.037 r_dihedral_angle_1_deg 5.728 r_angle_refined_deg 1.272 r_chiral_restr 0.099 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1713 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling MOLREP phasing