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Crystal structure of YfiB(L43P) in complex with YfiR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZHU 4ZHU, 4ZHW experimental model PDB 4ZHW 4ZHU, 4ZHW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10%(w/v) PEG 6000, 0.1 M Bicine pH 9.0
Crystal Properties Matthews coefficient Solvent content 2.48 50.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.798 α = 72.69 b = 58.413 β = 83.01 c = 70.324 γ = 89.33
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 2016-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9791 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 66.62 97.7 0.089 13 3.5 37342
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 2.2 2.27 95 0.462 3.6 3
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 4ZHU, 4ZHW 2.19 66.62 35314 1999 96.91 0.18015 0.17884 0.1889 0.20335 0.2073 RANDOM 49.794
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] 0.22 0.42 -0.96 -0.08 0.38 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.815 r_dihedral_angle_4_deg 15.834 r_dihedral_angle_3_deg 14.448 r_long_range_B_refined 7.98 r_long_range_B_other 7.926 r_dihedral_angle_1_deg 6.282 r_scangle_other 4.645 r_mcangle_it 3.595 r_mcangle_other 3.595 r_scbond_it 3.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.815 r_dihedral_angle_4_deg 15.834 r_dihedral_angle_3_deg 14.448 r_long_range_B_refined 7.98 r_long_range_B_other 7.926 r_dihedral_angle_1_deg 6.282 r_scangle_other 4.645 r_mcangle_it 3.595 r_mcangle_other 3.595 r_scbond_it 3.496 r_scbond_other 3.166 r_mcbond_it 2.435 r_mcbond_other 2.433 r_angle_refined_deg 1.543 r_angle_other_deg 0.986 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 4217 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing