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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, 1.4M Ammonium Tartrate Dibasic
Crystal Properties Matthews coefficient Solvent content 1.96 37.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.361 α = 90 b = 77.361 β = 90 c = 37.517 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) 1.00 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 1.65 20 100 0.096 0.1 0.03 8.6 11.6 14184
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 1.65 1.68 100 0.545 0.071 0.022 0.997 11.7 813
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 1.65 19.34 13431 675 99.6 0.181 0.178 0.1911 0.236 0.2394 RANDOM 25.88
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.887 r_dihedral_angle_4_deg 20.438 r_dihedral_angle_3_deg 13.729 r_dihedral_angle_1_deg 6.023 r_mcangle_it 2.675 r_mcbond_it 1.871 r_mcbond_other 1.841 r_angle_refined_deg 1.76 r_angle_other_deg 1.136 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.887 r_dihedral_angle_4_deg 20.438 r_dihedral_angle_3_deg 13.729 r_dihedral_angle_1_deg 6.023 r_mcangle_it 2.675 r_mcbond_it 1.871 r_mcbond_other 1.841 r_angle_refined_deg 1.76 r_angle_other_deg 1.136 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2) r_scbond_it SIDE-CHAIN BOND OTHER ATOMS (A**2) r_scangle_it SIDE-CHAIN ANGLE OTHER ATOMS (A**2) LONG RANGE B REFINED ATOMS (A**2) LONG RANGE B OTHER ATOMS (A**2) r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing PDB_EXTRACT data extraction HKL-2000 data reduction