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Lysozyme cluster 3 dual apo structure
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 2.05 40.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.23 α = 90 b = 79.23 β = 90 c = 37.52 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 92.4 0.36 0.869 2.34 2.99 14274
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 1.9 0.145
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 39.65 7920 431 98.28 0.20917 0.20604 0.2128 0.26479 0.2646 RANDOM 29.591
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] 2.38 2.38 -4.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.975 r_dihedral_angle_4_deg 19.528 r_dihedral_angle_3_deg 14.321 r_long_range_B_refined 9.734 r_long_range_B_other 9.282 r_dihedral_angle_1_deg 7.712 r_scangle_other 3.865 r_mcangle_other 2.973 r_mcangle_it 2.961 r_scbond_it 2.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.975 r_dihedral_angle_4_deg 19.528 r_dihedral_angle_3_deg 14.321 r_long_range_B_refined 9.734 r_long_range_B_other 9.282 r_dihedral_angle_1_deg 7.712 r_scangle_other 3.865 r_mcangle_other 2.973 r_mcangle_it 2.961 r_scbond_it 2.345 r_scbond_other 2.343 r_mcbond_it 1.853 r_mcbond_other 1.828 r_angle_refined_deg 1.42 r_angle_other_deg 1.252 r_chiral_restr 0.061 r_bond_refined_d 0.005 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