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Heme sensor protein PefR from Streptococcus agalactiae bound to operator DNA (28-mer)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DVS 7DVS, 4LLN experimental model PDB 4LLN 7DVS, 4LLN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 25%(w/v) PEGMME 2000, 0.2 M lithium sulfate, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 3.59 65.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.973 α = 90 b = 100.973 β = 90 c = 128.989 γ = 120
Symmetry Space Group P 32 1 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 16M mirrors 2018-01-22 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 2.49 47.06 99.9 0.083 0.089 0.999 14.63 6.992 26423 75.503
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 2.49 2.65 99.4 1.769 1.911 0.562 1 7.052
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7DVS, 4LLN 2.49 47.06 25129 1262 99.84 0.2189 0.2175 0.2463 0.2401 RANDOM 86.059
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] -1.34 -0.67 -1.34 4.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.945 r_dihedral_angle_3_deg 21.691 r_dihedral_angle_4_deg 11.82 r_dihedral_angle_1_deg 6.005 r_angle_refined_deg 1.885 r_chiral_restr 0.128 r_gen_planes_refined 0.012 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2267 Nucleic Acid Atoms 1148 Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction Coot model building XDS data reduction