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1.9 Angstrom Resolution Crystal Structure of Cupin_2 Domain (pfam 07883) of XRE Family Transcriptional Regulator from Enterobacter cloacae.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y9Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 Protein: 12.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5; Screen: 0.2M Sodium thiocyan, 20% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.97 58.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.269 α = 90 b = 66.269 β = 90 c = 116.319 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 100 CCD MARMOSAIC 300 mm CCD C(111) 2017-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.9 30 99.5 0.074 0.074 0.081 0.032 22.1 6.3 21115 -3 29.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.779 0.779 0.87 0.381 0.678 2.2 5.1
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 1Y9Q 1.9 29.87 20005 1056 99.66 0.18483 0.18284 0.1907 0.22046 0.2226 RANDOM 37.197
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] 0.57 0.57 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.575 r_dihedral_angle_4_deg 11.289 r_dihedral_angle_3_deg 10.265 r_long_range_B_refined 7.506 r_long_range_B_other 7.183 r_dihedral_angle_1_deg 3.285 r_scangle_other 2.425 r_mcangle_other 2.395 r_mcangle_it 2.394 r_angle_refined_deg 1.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.575 r_dihedral_angle_4_deg 11.289 r_dihedral_angle_3_deg 10.265 r_long_range_B_refined 7.506 r_long_range_B_other 7.183 r_dihedral_angle_1_deg 3.285 r_scangle_other 2.425 r_mcangle_other 2.395 r_mcangle_it 2.394 r_angle_refined_deg 1.474 r_mcbond_it 1.456 r_scbond_it 1.455 r_mcbond_other 1.454 r_scbond_other 1.454 r_angle_other_deg 0.802 r_chiral_restr 0.097 r_gen_planes_refined 0.017 r_gen_planes_other 0.013 r_bond_refined_d 0.009 r_bond_other_d 0.002 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 1530 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing