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Structure of Hen egg white lysozyme soaked with Ni2-Xylylbicyclam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 277 Acetate buffer, NaCl , pH 4.5, VAPOR DIFFUSION, temperature 277K, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.01 38.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.577 α = 90 b = 77.577 β = 90 c = 38.355 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.75 34.38 99.9 11704
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1YIL 1.75 34.38 12329 11704 587 99.9 0.184 0.18659 0.184 0.1808 0.23214 0.2264 RANDOM 25.685
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.85 r_dihedral_angle_4_deg 19.865 r_dihedral_angle_3_deg 13.096 r_dihedral_angle_1_deg 6.087 r_scangle_it 4.437 r_scbond_it 2.937 r_mcangle_it 1.952 r_angle_refined_deg 1.795 r_mcbond_it 1.11 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.85 r_dihedral_angle_4_deg 19.865 r_dihedral_angle_3_deg 13.096 r_dihedral_angle_1_deg 6.087 r_scangle_it 4.437 r_scbond_it 2.937 r_mcangle_it 1.952 r_angle_refined_deg 1.795 r_mcbond_it 1.11 r_nbtor_refined 0.295 r_symmetry_hbond_refined 0.215 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.183 r_metal_ion_refined 0.158 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1007 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement