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X-ray structure of NeoB from Streptomyces fradiae in complex with PMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 14-18% PEG-8000, 200 mM tetraethylammonium chloride, 200 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.64 53.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.726 α = 75.59 b = 82.705 β = 88.85 c = 100.86 γ = 70.6
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 210r 2017-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9794 APS 19-BM
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 1.75 97.45 96.5 0.094 0.094 39.3 3.4 179314
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 94.2 0.309 0.309 9.6 2.9
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 6CBO 1.75 97.46 170495 8819 95.9 0.17623 0.17458 0.1882 0.20762 0.2187 RANDOM 26.939
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] 3.35 0.76 -0.89 -0.13 0.49 -1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.841 r_dihedral_angle_4_deg 17.749 r_dihedral_angle_3_deg 15.76 r_long_range_B_refined 6.528 r_long_range_B_other 6.528 r_dihedral_angle_1_deg 6.252 r_scangle_other 5.628 r_scbond_it 3.902 r_scbond_other 3.901 r_mcangle_it 3.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.841 r_dihedral_angle_4_deg 17.749 r_dihedral_angle_3_deg 15.76 r_long_range_B_refined 6.528 r_long_range_B_other 6.528 r_dihedral_angle_1_deg 6.252 r_scangle_other 5.628 r_scbond_it 3.902 r_scbond_other 3.901 r_mcangle_it 3.451 r_mcangle_other 3.451 r_mcbond_it 2.695 r_mcbond_other 2.692 r_angle_refined_deg 1.62 r_angle_other_deg 0.866 r_chiral_restr 0.11 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 12591 Nucleic Acid Atoms Solvent Atoms 971 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing