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Hen egg-white lysozyme structure from a spent-beam experiment at LCLS: refocused beam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ET8 PDB ENTRY 4ET8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 3 293 After crystallization, the solution used for growing the crystals (20 % NaCl, 6 % PEG 6000, 1 M Na acetate pH 3.0) was exchanged for storage solution (10 % NaCl, 1.0 M Na acetate pH 3.4)
, batch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.02 α = 90 b = 79.02 β = 90 c = 38.17 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 293 PIXEL CSPAD KB mirrors 2012-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.63 SLAC LCLS CXI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 40 100 5742 5742
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.4 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 4ET8 2.3 39.55 5451 5451 291 99.95 0.20677 0.20677 0.20431 0.2015 0.2508 0.2599 RANDOM, SAME TEST SET AS 4ET8 38.018
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] -0.29 -0.29 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.875 r_dihedral_angle_3_deg 13.012 r_dihedral_angle_4_deg 12.898 r_dihedral_angle_1_deg 5.722 r_scangle_it 2.102 r_scbond_it 1.202 r_angle_refined_deg 0.968 r_angle_other_deg 0.843 r_mcangle_it 0.73 r_mcbond_it 0.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.875 r_dihedral_angle_3_deg 13.012 r_dihedral_angle_4_deg 12.898 r_dihedral_angle_1_deg 5.722 r_scangle_it 2.102 r_scbond_it 1.202 r_angle_refined_deg 0.968 r_angle_other_deg 0.843 r_mcangle_it 0.73 r_mcbond_it 0.358 r_chiral_restr 0.055 r_mcbond_other 0.049 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other 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 1001 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 2
Software Software Software Name Purpose LCLS data collection REFMAC refinement CrystFEL data reduction CrystFEL data scaling REFMAC phasing