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Crystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with benzamidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ICH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 293 0.2 M tri-Potassium Citrate, 20% PEG3350, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.98 37.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.791 α = 90 b = 109.952 β = 90 c = 76.875 γ = 90
Symmetry Space Group C 2 2 21
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 MIRROR 2012-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07815 APS 21-ID-D
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 2.35 30 96.1 0.059 53.4 6.9 7525 7525 -3 57
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 2.35 2.39 100 0.14 17.7 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4ICH 2.35 27.85 7166 7166 344 95.79 0.20167 0.19836 0.2007 0.26586 0.2709 RANDOM 59.308
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] 2.25 -3.03 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.213 r_dihedral_angle_3_deg 17.619 r_dihedral_angle_4_deg 16.557 r_dihedral_angle_1_deg 5.434 r_angle_refined_deg 1.733 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.213 r_dihedral_angle_3_deg 17.619 r_dihedral_angle_4_deg 16.557 r_dihedral_angle_1_deg 5.434 r_angle_refined_deg 1.733 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 1568 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 13
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing