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Lysozyme bound to 3-Aminophenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 10uL of 50mM 3-aminophenol was deposited on a cover slip and allowed to dry. A 20 uL pellet of 4% sodium chloride + 5% ethylene glycol + 10% glycerol in 2% agar was deposited on the cover slip. Adjacent to this was positioned lysozyme (10 ul of 30 mg/ml lysozyme in 100 mM sodium acetate pH 4.6). The cover slip was equilibrated over precipitant containing all the crystallization components.
Crystal Properties Matthews coefficient Solvent content 2.08 40.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.085 α = 90 b = 80.085 β = 90 c = 37.197 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 PIXEL DECTRIS EIGER X 9M 2018-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9202 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.35 28.31 99.7 0.068 0.998 21.9 12.8 25655
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.39 96 0.725 0.906 3.2 11.3
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 4N8Z 1.35 28.31 25655 1359 99.67 0.15898 0.15754 0.1573 0.1859 0.1883 RANDOM 18.817
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 35.789 r_dihedral_angle_4_deg 21.61 r_dihedral_angle_3_deg 13.121 r_long_range_B_refined 7.025 r_long_range_B_other 6.982 r_dihedral_angle_1_deg 6.426 r_scangle_other 4.437 r_scbond_other 2.977 r_scbond_it 2.976 r_angle_refined_deg 2.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.789 r_dihedral_angle_4_deg 21.61 r_dihedral_angle_3_deg 13.121 r_long_range_B_refined 7.025 r_long_range_B_other 6.982 r_dihedral_angle_1_deg 6.426 r_scangle_other 4.437 r_scbond_other 2.977 r_scbond_it 2.976 r_angle_refined_deg 2.533 r_mcangle_other 2.169 r_mcangle_it 2.152 r_mcbond_it 1.54 r_mcbond_other 1.474 r_angle_other_deg 1.276 r_chiral_restr 0.171 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 r_scangle_it 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 218 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing