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Lysozyme structure at room temperature by serial synchrotron crystallography with COC chips
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 295 6% (w/v) PEG 6000, 0.1 M sodium acetate pH 3.0, 20% (w/v) sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.08 40.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.3 α = 90 b = 78.3 β = 90 c = 38.1 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 PIXEL PSI JUNGFRAU 4M 2024-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.072 ESRF ID29
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.6 39.15 100 0.158 5 4.51 16156
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 1.563
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 1.6 39.15 15322 834 99.98 0.19378 0.1908 0.1932 0.25057 0.2289 RANDOM 25.364
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.284 r_dihedral_angle_2_deg 7.801 r_dihedral_angle_1_deg 6.732 r_long_range_B_refined 6.693 r_long_range_B_other 6.66 r_scangle_other 5.663 r_scbond_it 3.679 r_scbond_other 3.677 r_mcangle_other 2.779 r_mcangle_it 2.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.284 r_dihedral_angle_2_deg 7.801 r_dihedral_angle_1_deg 6.732 r_long_range_B_refined 6.693 r_long_range_B_other 6.66 r_scangle_other 5.663 r_scbond_it 3.679 r_scbond_other 3.677 r_mcangle_other 2.779 r_mcangle_it 2.758 r_mcbond_it 2.017 r_mcbond_other 2.008 r_angle_refined_deg 1.597 r_angle_other_deg 0.565 r_chiral_restr 0.075 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 1010 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction CrystFEL data scaling MOLREP phasing