☰ Navigation Tabs
Crystal structure of heme sensor protein PefR from Streptococcus agalactiae in complex with heme
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 35%(v/v) MPD, 0.2 M KCl, 50 mM hexamine cobalt(III) chloride, 50 mM MES
Crystal Properties Matthews coefficient Solvent content 2.37 48.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.899 α = 90 b = 32.149 β = 95.07 c = 76.654 γ = 90
Symmetry Space Group C 1 2 1
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 16M mirrors 2017-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.7 29.13 97.1 0.049 0.054 0.999 16.27 6.591 18070 51.157
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 95.5 0.954 1.03 0.853 1.47 6.989
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.7 29.13 17175 882 96.99 0.2386 0.2366 0.243 0.285 0.2927 RANDOM 50.487
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] 0.38 -1.32 1.22 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.703 r_dihedral_angle_4_deg 21.646 r_dihedral_angle_3_deg 16.781 r_dihedral_angle_1_deg 4.973 r_angle_refined_deg 1.948 r_angle_other_deg 1.466 r_chiral_restr 0.092 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.703 r_dihedral_angle_4_deg 21.646 r_dihedral_angle_3_deg 16.781 r_dihedral_angle_1_deg 4.973 r_angle_refined_deg 1.948 r_angle_other_deg 1.466 r_chiral_restr 0.092 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1196 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 44
Software Software Software Name Purpose XSCALE data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction