☰ Navigation Tabs
Hen egg-white lysozyme phased using free-electron laser data
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VDS PDB ENTRY 1VDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 3 293 20 % NaCl, 6 % PEG 6000, 1 M Na acetate pH 3.0, stored in 8% NaCl, 0.1 M sodium acetate buffer, pH 4.0, soaked in storage solution + 100 mM gadoteridol, batch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.1 α = 90 b = 79.1 β = 90 c = 39.2 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 Cornell-SLAC Pixel Array Detector (CSPAD) 2013-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.45 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 2.1 40 100 7294
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 (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 PDB ENTRY 1VDS 2.1 39.55 7287 7294 385 99.99 0.2322 0.23098 0.2241 0.25632 0.251 RANDOM 32.54
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] -0.27 -0.27 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.663 r_dihedral_angle_4_deg 18.229 r_dihedral_angle_3_deg 14.043 r_dihedral_angle_1_deg 5.711 r_scangle_it 2.224 r_scbond_it 1.347 r_angle_refined_deg 1.285 r_mcangle_it 0.862 r_angle_other_deg 0.841 r_mcbond_it 0.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.663 r_dihedral_angle_4_deg 18.229 r_dihedral_angle_3_deg 14.043 r_dihedral_angle_1_deg 5.711 r_scangle_it 2.224 r_scbond_it 1.347 r_angle_refined_deg 1.285 r_mcangle_it 0.862 r_angle_other_deg 0.841 r_mcbond_it 0.435 r_mcbond_other 0.08 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 992 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 58
Software Software Software Name Purpose DAQ data collection PHASER phasing REFMAC refinement CrystFEL data reduction CrystFEL data scaling