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Spectroscopically-validated structure of DtpB from Streptomyces lividans in the ferric state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other SFX structure of ferric DtpB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 291 6-10 mg/mL of protein in 50mM Sodium acteate, 150mM NaCl pH 5 mixed with 100 mM MgCl2, 100 mM HEPES pH 7.5, 16% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.47 50.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.79 α = 90 b = 120.27 β = 90 c = 196.01 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 PIXEL DECTRIS PILATUS 6M-F 2019-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.8 SLS X10SA
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 1.99 49.05 99.2 0.227 0.971 7.5 6.9 138089 28.2
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 1.99 2.02 97.1 1.02 0.498 2.1 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 SFX structure of ferric DtpB 1.99 49.05 131265 6824 99.04 0.1782 0.1761 0.1855 0.2179 0.2243 RANDOM 30.279
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] -0.1 0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.472 r_dihedral_angle_4_deg 17.602 r_dihedral_angle_3_deg 12.44 r_dihedral_angle_1_deg 7.322 r_angle_refined_deg 1.584 r_angle_other_deg 1.35 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.472 r_dihedral_angle_4_deg 17.602 r_dihedral_angle_3_deg 12.44 r_dihedral_angle_1_deg 7.322 r_angle_refined_deg 1.584 r_angle_other_deg 1.35 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13912 Nucleic Acid Atoms Solvent Atoms 1142 Heterogen Atoms 375
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling REFMAC phasing