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Crystal structure of hen egg white lysozyme at 200 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 2.03 39.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.11 α = 90 b = 79.11 β = 90 c = 37.176 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 200 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 22.29 99.37 0.677 12.69 1.9 19510
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 0.677
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 22.29 19510 997 99.48 0.169 0.1669 0.2298 0.2016 0.2477 9.573
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 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.114 r_dihedral_angle_4_deg 17.233 r_dihedral_angle_3_deg 14.512 r_dihedral_angle_1_deg 6.751 r_lrange_it 4.041 r_lrange_other 3.845 r_scangle_it 2.918 r_scangle_other 2.916 r_scbond_it 1.944 r_scbond_other 1.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.114 r_dihedral_angle_4_deg 17.233 r_dihedral_angle_3_deg 14.512 r_dihedral_angle_1_deg 6.751 r_lrange_it 4.041 r_lrange_other 3.845 r_scangle_it 2.918 r_scangle_other 2.916 r_scbond_it 1.944 r_scbond_other 1.943 r_angle_refined_deg 1.838 r_angle_other_deg 1.626 r_mcangle_other 1.163 r_mcangle_it 1.16 r_mcbond_it 0.753 r_mcbond_other 0.741 r_nbd_refined 0.247 r_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.174 r_nbd_other 0.151 r_symmetry_xyhbond_nbd_refined 0.131 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.087 r_symmetry_nbd_refined 0.055 r_metal_ion_refined 0.054 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 143 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction