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Crystal structure of hen egg white lysozyme at 275 Kelvin (Duplicate)
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 2.07 40.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.723 α = 90 b = 79.723 β = 90 c = 37.427 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 275 CMOS BRUKER PHOTON 100 2020-11-04 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 22.53 93.86 0.683 8.03 1.86 19138
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 22.53 0.683
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3A8Z 1.5 22.526 19138 973 93.86 0.232 0.2301 0.2597 0.1892 21.402
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] -0.009 -0.009 0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.215 r_dihedral_angle_4_deg 22.774 r_dihedral_angle_3_deg 14.562 r_dihedral_angle_1_deg 7.041 r_lrange_it 5.605 r_lrange_other 5.604 r_scangle_it 4.479 r_scangle_other 4.476 r_scbond_it 2.985 r_scbond_other 2.983
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.215 r_dihedral_angle_4_deg 22.774 r_dihedral_angle_3_deg 14.562 r_dihedral_angle_1_deg 7.041 r_lrange_it 5.605 r_lrange_other 5.604 r_scangle_it 4.479 r_scangle_other 4.476 r_scbond_it 2.985 r_scbond_other 2.983 r_mcangle_other 2.591 r_mcangle_it 2.589 r_mcbond_it 1.947 r_mcbond_other 1.936 r_angle_refined_deg 1.861 r_angle_other_deg 1.485 r_metal_ion_refined 0.26 r_nbd_other 0.235 r_nbd_refined 0.232 r_symmetry_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.195 r_symmetry_nbd_refined 0.193 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.015 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction