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Crystal structure of hen egg white lysozyme at 150 Kelvin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 295 1.2 M NaCl and 100 mM AcONa pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.01 38.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.719 α = 90 b = 78.719 β = 90 c = 37.158 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 150 CMOS BRUKER PHOTON 100 2020-10-13 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER TURBO X-RAY SOURCE 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.5 22.29 99.68 0.736 9.58 1.9 19294
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 22.29 0.736
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3A8Z 1.5 22.286 19294 988 99.685 0.172 0.1702 0.1785 0.209 0.2126 11.514
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] 0.001 0.001 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.145 r_dihedral_angle_4_deg 19.11 r_dihedral_angle_3_deg 11.984 r_dihedral_angle_1_deg 6.519 r_lrange_it 4.36 r_lrange_other 4.298 r_scangle_it 3.125 r_scangle_other 3.123 r_scbond_it 2.203 r_scbond_other 2.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.145 r_dihedral_angle_4_deg 19.11 r_dihedral_angle_3_deg 11.984 r_dihedral_angle_1_deg 6.519 r_lrange_it 4.36 r_lrange_other 4.298 r_scangle_it 3.125 r_scangle_other 3.123 r_scbond_it 2.203 r_scbond_other 2.202 r_angle_refined_deg 1.88 r_angle_other_deg 1.64 r_mcangle_other 1.514 r_mcangle_it 1.513 r_mcbond_it 1.012 r_mcbond_other 0.98 r_nbd_refined 0.255 r_symmetry_nbd_other 0.204 r_symmetry_xyhbond_nbd_refined 0.192 r_nbd_other 0.182 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.102 r_symmetry_nbd_refined 0.097 r_symmetry_nbtor_other 0.087 r_metal_ion_refined 0.064 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction