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Lysozyme cluster 0062 (NAG and benzamidine ligands)
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 4.6 290 4% SODIUM CHLORIDE, 100MM SODIUM
ACETATE PH 4.6, 120MG/ML
Crystal Properties Matthews coefficient Solvent content 2.03 39.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.78 α = 90 b = 78.78 β = 90 c = 37.57 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 2016-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92 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 2 50 97.9 0.408 0.859 3.73 5.08 14987
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 2 2.12 1.47 0.254
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 2 39.42 7918 440 99.28 0.19003 0.18734 0.1954 0.23738 0.2456 RANDOM 20.413
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] 0.11 0.11 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.855 r_dihedral_angle_4_deg 19.01 r_dihedral_angle_3_deg 14.475 r_long_range_B_refined 8.67 r_dihedral_angle_1_deg 7.494 r_long_range_B_other 7.414 r_scangle_other 3.616 r_mcangle_other 2.227 r_mcangle_it 2.198 r_scbond_it 2.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.855 r_dihedral_angle_4_deg 19.01 r_dihedral_angle_3_deg 14.475 r_long_range_B_refined 8.67 r_dihedral_angle_1_deg 7.494 r_long_range_B_other 7.414 r_scangle_other 3.616 r_mcangle_other 2.227 r_mcangle_it 2.198 r_scbond_it 2.188 r_scbond_other 2.186 r_angle_refined_deg 1.605 r_mcbond_it 1.43 r_angle_other_deg 1.379 r_mcbond_other 1.309 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 210 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing