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Human Gamma-D Crystallin R36S fresh serial crystallographic structure
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HK0
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 2.58 52.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.6 α = 90 b = 83.7 β = 90 c = 100.4 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 PILATUS 6M 2021-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.99 Diamond I24
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 2.1 38.66 99.9 0.974 0.19 3.87 26.7 50856
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 2.1 2.14 0.49 1.64 0.95
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 38.66 25669 1317 99.67 0.20624 0.2037 0.2115 0.25783 0.2568 RANDOM 37.965
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] -0.64 -0.07 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.42 r_dihedral_angle_2_deg 14.232 r_long_range_B_other 11.283 r_long_range_B_refined 11.28 r_scangle_other 7.897 r_dihedral_angle_1_deg 6.899 r_scbond_it 5.046 r_scbond_other 5.044 r_mcangle_other 4.481 r_mcangle_it 4.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.42 r_dihedral_angle_2_deg 14.232 r_long_range_B_other 11.283 r_long_range_B_refined 11.28 r_scangle_other 7.897 r_dihedral_angle_1_deg 6.899 r_scbond_it 5.046 r_scbond_other 5.044 r_mcangle_other 4.481 r_mcangle_it 4.48 r_mcbond_it 3.041 r_mcbond_other 3.034 r_angle_refined_deg 1.45 r_angle_other_deg 0.506 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 2887 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystFEL data scaling CrystFEL data reduction MOLREP phasing