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Crystal structure of a predicted dna-binding transcriptional regulator (saro_1072) from novosphingobium aromaticivorans dsm at 2.10 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QTQ PDB entry 2QTQ chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 NANODROP, 1.6M (NH4)2SO4, 0.1M Citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 6.01 79.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.837 α = 90 b = 102.837 β = 90 c = 111.276 γ = 90
Symmetry Space Group P 43 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 325 mm CCD Flat mirror (vertical focusing) 2007-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 1.00000 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 29.185 99.8 0.081 0.081 6.8 4.8 35346 39.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 100 0.816 0.816 0.9 4.9 2560
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 PDB entry 2QTQ chain A 2.1 29.185 35315 1772 99.65 0.172 0.17 0.1742 0.202 0.2025 RANDOM 35.675
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] -1.16 -1.16 2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.005 r_dihedral_angle_4_deg 22.999 r_dihedral_angle_3_deg 14.614 r_scangle_it 8.367 r_scbond_it 6.549 r_dihedral_angle_1_deg 5.285 r_mcangle_it 3.212 r_mcbond_it 2.438 r_angle_refined_deg 1.649 r_angle_other_deg 1.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.005 r_dihedral_angle_4_deg 22.999 r_dihedral_angle_3_deg 14.614 r_scangle_it 8.367 r_scbond_it 6.549 r_dihedral_angle_1_deg 5.285 r_mcangle_it 3.212 r_mcbond_it 2.438 r_angle_refined_deg 1.649 r_angle_other_deg 1.061 r_mcbond_other 0.481 r_symmetry_vdw_other 0.315 r_symmetry_hbond_refined 0.243 r_nbd_refined 0.212 r_nbd_other 0.197 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.173 r_symmetry_vdw_refined 0.143 r_chiral_restr 0.1 r_nbtor_other 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1612 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction EPMR phasing