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Hen egg lysozyme at room temperature solved from dataset acquired by oscillation method
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XJB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 Na acetate, MPEG 5K, NaCl, Na acetate, ethylene glycerol
Crystal Properties Matthews coefficient Solvent content 2.1 41.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.02 α = 90 b = 80.02 β = 90 c = 37.69 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 DECTRIS PILATUS 6M 2015-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 1.2 50 99.9 0.063 0.058 11.19 6.56 477708 72771
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 (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 4XJB 1.8 40.01 11243 592 99.97 0.15218 0.14976 0.1629 0.19893 0.207 RANDOM 23.79
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] -0.59 -0.59 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.31 r_dihedral_angle_4_deg 19.307 r_dihedral_angle_3_deg 14.315 r_long_range_B_refined 8.525 r_long_range_B_other 8.521 r_scangle_other 7.204 r_dihedral_angle_1_deg 6.079 r_scbond_it 4.641 r_scbond_other 4.637 r_mcangle_other 3.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.31 r_dihedral_angle_4_deg 19.307 r_dihedral_angle_3_deg 14.315 r_long_range_B_refined 8.525 r_long_range_B_other 8.521 r_scangle_other 7.204 r_dihedral_angle_1_deg 6.079 r_scbond_it 4.641 r_scbond_other 4.637 r_mcangle_other 3.213 r_mcangle_it 3.207 r_mcbond_it 2.333 r_mcbond_other 2.308 r_angle_refined_deg 2.036 r_angle_other_deg 1.187 r_chiral_restr 0.141 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1000 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing