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Crystal structure of lysozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M Tris-HCl pH8.5, 1.3M Ammonium Tartrate Dibasic
Crystal Properties Matthews coefficient Solvent content 1.93 36.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.956 α = 90 b = 76.956 β = 90 c = 37.382 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 100 CCD ADSC QUANTUM 315r 2016-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.0 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.24 50 99.9 0.06 0.063 0.019 13 11.2 32317
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.24 1.26 99.8 0.673 0.706 0.213 0.882 10.8 1584
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 193L 1.24 38.478 30689 1577 99.83 0.1355 0.1336 0.133 0.1728 0.1725 RANDOM 18.324
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] 0.03 0.03 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.935 r_sphericity_free 25.001 r_dihedral_angle_4_deg 21.568 r_dihedral_angle_3_deg 13.025 r_sphericity_bonded 10.964 r_dihedral_angle_1_deg 5.92 r_rigid_bond_restr 2.839 r_angle_refined_deg 1.761 r_mcangle_it 1.744 r_mcbond_it 1.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.935 r_sphericity_free 25.001 r_dihedral_angle_4_deg 21.568 r_dihedral_angle_3_deg 13.025 r_sphericity_bonded 10.964 r_dihedral_angle_1_deg 5.92 r_rigid_bond_restr 2.839 r_angle_refined_deg 1.761 r_mcangle_it 1.744 r_mcbond_it 1.399 r_mcbond_other 1.343 r_angle_other_deg 1.177 r_chiral_restr 0.131 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing PDB_EXTRACT data extraction HKL-2000 data reduction