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Lysozyme cluster 0028 (benzamidine ligand)
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 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.59 α = 90 b = 79.59 β = 90 c = 37.76 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 93.7 0.426 0.861 2.1 3.64 14696
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 2.01 0.159
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 39.83 7989 441 97.81 0.21057 0.20781 0.211 0.26192 0.2619 RANDOM 31.162
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] -0.52 -0.52 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.866 r_dihedral_angle_4_deg 20.27 r_dihedral_angle_3_deg 14.405 r_long_range_B_refined 10.317 r_long_range_B_other 9.496 r_dihedral_angle_1_deg 7.679 r_scangle_other 4.79 r_mcangle_other 3.023 r_mcangle_it 3.013 r_scbond_it 2.853
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.866 r_dihedral_angle_4_deg 20.27 r_dihedral_angle_3_deg 14.405 r_long_range_B_refined 10.317 r_long_range_B_other 9.496 r_dihedral_angle_1_deg 7.679 r_scangle_other 4.79 r_mcangle_other 3.023 r_mcangle_it 3.013 r_scbond_it 2.853 r_scbond_other 2.85 r_mcbond_it 1.924 r_mcbond_other 1.903 r_angle_refined_deg 1.482 r_angle_other_deg 1.263 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 213 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing