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Crystal Structure of Wild-type Mouse Gamma(S)-Crystallin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VH1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.1 M HEPES, 0.5% v/v Jeffamine
Crystal Properties Matthews coefficient Solvent content 2.97 58.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.056 α = 90 b = 74.056 β = 90 c = 79.437 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277.15 PIXEL DECTRIS EIGER X 9M 2024-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.97856 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.83 49.95 98.91 0.589 0.678 0.331 0.374 8.4 2.1 38290
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 1.9 1.93 2.267 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.83 49.95 21452 1135 98.91 0.16793 0.16657 0.19278 0.2053 RANDOM 20.17
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] 0.5 0.25 0.5 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.626 r_dihedral_angle_2_deg 8.752 r_long_range_B_other 8.457 r_long_range_B_refined 8.445 r_scangle_other 6.703 r_dihedral_angle_1_deg 6.409 r_scbond_it 4.256 r_scbond_other 4.253 r_mcangle_it 2.764 r_mcangle_other 2.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.626 r_dihedral_angle_2_deg 8.752 r_long_range_B_other 8.457 r_long_range_B_refined 8.445 r_scangle_other 6.703 r_dihedral_angle_1_deg 6.409 r_scbond_it 4.256 r_scbond_other 4.253 r_mcangle_it 2.764 r_mcangle_other 2.762 r_mcbond_it 1.972 r_mcbond_other 1.965 r_angle_refined_deg 1.744 r_angle_other_deg 0.624 r_chiral_restr 0.099 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1491 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing