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Human Gamma-D crystallin R36S mutant after UV illumination
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G98 2G98
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.8 298 50 mM phosphate buffer pH 7.8, 20 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.9 α = 90 b = 83.7 β = 90 c = 101 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL DECTRIS EIGER X 16M 2019-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.98 PETRA III, EMBL c/o DESY P14 (MX2)
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 25600 25600
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 2 101 100 0.9546 0.2277 3.19 70.2 31633
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 100 0.2283 1.669 0.68 48.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2G98 2 101 27049 1746 85.666 0.2 0.1973 0.204 0.2407 0.2466 37.112
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] -0.682 0.323 0.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.712 r_dihedral_angle_4_deg 19.903 r_dihedral_angle_3_deg 16.439 r_lrange_it 9.474 r_lrange_other 9.473 r_dihedral_angle_1_deg 6.834 r_scangle_it 6.381 r_scangle_other 6.38 r_scbond_it 3.92 r_scbond_other 3.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.712 r_dihedral_angle_4_deg 19.903 r_dihedral_angle_3_deg 16.439 r_lrange_it 9.474 r_lrange_other 9.473 r_dihedral_angle_1_deg 6.834 r_scangle_it 6.381 r_scangle_other 6.38 r_scbond_it 3.92 r_scbond_other 3.919 r_mcangle_it 3.848 r_mcangle_other 3.848 r_mcbond_it 2.555 r_mcbond_other 2.541 r_angle_refined_deg 1.446 r_angle_other_deg 1.24 r_symmetry_xyhbond_nbd_refined 0.215 r_symmetry_nbd_other 0.186 r_nbd_other 0.179 r_nbd_refined 0.174 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.143 r_symmetry_nbd_refined 0.098 r_ncsr_local_group_1 0.086 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2871 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling MOLREP phasing