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PrfA, Transcriptional Regulator In Listeria Monocytogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OMI PDB ENTRY 1OMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 20 % (W/V) PEG 6000 100 MM NA-MES PH6.5 1 M LICL, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.951 α = 90 b = 80.713 β = 111.91 c = 60.965 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH RH-COATED SILICON MIRROR 2003-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 2.7 30 89 0.01 10.6 1.76 12402 1
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 2.7 2.8 68.9 0.03 3.1 2.1
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 PDB ENTRY 1OMI 2.7 56.8 11790 602 91.9 0.246 0.244 0.2438 0.289 0.2962 RANDOM 22.92
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] 4.66 8.23 -2.29 3.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.823 r_dihedral_angle_3_deg 17.854 r_dihedral_angle_4_deg 17.653 r_dihedral_angle_1_deg 5.433 r_scangle_it 3.616 r_mcangle_it 3.224 r_scbond_it 2.501 r_mcbond_it 2.288 r_angle_refined_deg 1.944 r_angle_other_deg 1.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.823 r_dihedral_angle_3_deg 17.854 r_dihedral_angle_4_deg 17.653 r_dihedral_angle_1_deg 5.433 r_scangle_it 3.616 r_mcangle_it 3.224 r_scbond_it 2.501 r_mcbond_it 2.288 r_angle_refined_deg 1.944 r_angle_other_deg 1.382 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.193 r_symmetry_vdw_other 0.183 r_nbtor_refined 0.176 r_nbd_other 0.162 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.148 r_chiral_restr 0.145 r_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.006 r_bond_other_d 0.004 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3740 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing