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IclR transcription factor complexed with 4-hydroxybenzoic acid from Microbacterium hydrocarbonoxydans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MES monohydrate, pH 6.5, 0.1 M sodium phosphate monobasic monohydrate, 0.1 M potassium phosphate monobasic and 2.0 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 3 58.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.08 α = 90 b = 83.08 β = 90 c = 203.89 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2016-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 2 50 99.9 0.09 1 19.8 7.2 49164
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 2 2.05 0.848 0.87 2.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5h1a 2 44.484 49157 2407 99.927 0.203 0.2019 0.2099 0.2179 0.2236 29.131
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] 1.362 1.362 -2.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.91 r_dihedral_angle_4_deg 18.114 r_dihedral_angle_3_deg 14.477 r_dihedral_angle_1_deg 6.349 r_lrange_it 5.51 r_lrange_other 5.471 r_scangle_it 3.873 r_scangle_other 3.872 r_mcangle_it 2.654 r_mcangle_other 2.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.91 r_dihedral_angle_4_deg 18.114 r_dihedral_angle_3_deg 14.477 r_dihedral_angle_1_deg 6.349 r_lrange_it 5.51 r_lrange_other 5.471 r_scangle_it 3.873 r_scangle_other 3.872 r_mcangle_it 2.654 r_mcangle_other 2.654 r_scbond_it 2.368 r_scbond_other 2.367 r_mcbond_it 1.678 r_mcbond_other 1.667 r_angle_refined_deg 1.363 r_angle_other_deg 1.326 r_symmetry_nbd_refined 0.213 r_nbd_refined 0.203 r_symmetry_nbd_other 0.186 r_nbd_other 0.185 r_symmetry_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.147 r_xyhbond_nbd_refined 0.134 r_symmetry_xyhbond_nbd_other 0.118 r_symmetry_nbtor_other 0.078 r_xyhbond_nbd_other 0.077 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3659 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing