☰ Navigation Tabs
Crystal Structure of NadE from Streptococcus pyogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HUH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 0.1 M Tris, 20% PEG 4000, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.19 43.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.786 α = 90 b = 92.964 β = 90 c = 128.355 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2014-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97915 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 2.1 40 91.8 0.109 0.109 11.9 5.6 32708 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 90.5 0.772 2.3 5
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 5HUH 2.1 39.34 31017 1632 91.7 0.1589 0.15618 0.1682 0.21068 0.2131 RANDOM 33.058
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] -0.48 1 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.863 r_dihedral_angle_4_deg 22.759 r_dihedral_angle_3_deg 12.825 r_long_range_B_refined 5.947 r_long_range_B_other 5.876 r_dihedral_angle_1_deg 5.657 r_scangle_other 4.329 r_mcangle_it 3.006 r_mcangle_other 3.006 r_scbond_it 2.718
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.863 r_dihedral_angle_4_deg 22.759 r_dihedral_angle_3_deg 12.825 r_long_range_B_refined 5.947 r_long_range_B_other 5.876 r_dihedral_angle_1_deg 5.657 r_scangle_other 4.329 r_mcangle_it 3.006 r_mcangle_other 3.006 r_scbond_it 2.718 r_scbond_other 2.718 r_mcbond_it 1.938 r_mcbond_other 1.938 r_angle_refined_deg 1.877 r_angle_other_deg 1.469 r_chiral_restr 0.113 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.006 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 4019 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing