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Crystal structure of an IclR homolog complexed with 4-hydroxybenzoate from Microbacterium hydrocarbonoxydans in P212121 form
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 293 0.1 M MES, pH 6.5, 0.1 M sodium phosphate monobasic monohydrate, 0.1 M potassium phosphate monobasic, 2.0 M sodium chloride, and 1 mM 4-HBA
Crystal Properties Matthews coefficient Solvent content 2.09 41.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.071 α = 90 b = 74.642 β = 90 c = 104.097 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 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 2.1 50 94.6 0.097 1 19.1 3.8 27794
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 2.1 2.14 0.608 0.79 2.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5H1A 2.101 48.222 27755 1405 94.559 0.215 0.2147 0.2189 0.2079 35.58
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] 3.496 -0.716 -2.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.927 r_dihedral_angle_4_deg 20.097 r_dihedral_angle_3_deg 15.222 r_dihedral_angle_1_deg 6.404 r_lrange_it 4.561 r_lrange_other 4.561 r_scangle_it 3.254 r_scangle_other 3.253 r_mcangle_it 2.458 r_mcangle_other 2.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.927 r_dihedral_angle_4_deg 20.097 r_dihedral_angle_3_deg 15.222 r_dihedral_angle_1_deg 6.404 r_lrange_it 4.561 r_lrange_other 4.561 r_scangle_it 3.254 r_scangle_other 3.253 r_mcangle_it 2.458 r_mcangle_other 2.458 r_scbond_it 2.014 r_scbond_other 2.013 r_mcbond_it 1.53 r_mcbond_other 1.524 r_angle_refined_deg 1.291 r_angle_other_deg 1.222 r_symmetry_nbd_refined 0.369 r_symmetry_xyhbond_nbd_other 0.331 r_nbd_other 0.256 r_nbd_refined 0.198 r_symmetry_nbd_other 0.196 r_xyhbond_nbd_refined 0.162 r_nbtor_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.135 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.058 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3654 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MoRDa phasing