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Structural basis of the nucleotide driven conformational changes in the AAA domain of transcription activator PspF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BJW PDB ENTRY 2BJW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 2M AMMONIUM FORMATE, 0.1 M HEPES PH 8.0, 5% MPD
Crystal Properties Matthews coefficient Solvent content 2.33 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.027 α = 90 b = 113.027 β = 90 c = 39.436 γ = 120
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 ADSC CCD MIRRORS 2004-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.8 100 97.8 0.05 24 6 26570 3
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 1.8 1.86 93.5 0.37 2.8 3.3
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 2BJW 1.8 100 25139 1280 97.8 0.208 0.206 0.2142 0.246 0.2543 RANDOM 21.3
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] -0.85 -0.42 -0.85 1.27
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.326 r_dihedral_angle_1_deg 5.975 r_scbond_it 3.936 r_mcangle_it 2.596 r_angle_refined_deg 2.102 r_mcbond_it 1.495 r_angle_other_deg 1.006 r_symmetry_vdw_other 0.353 r_symmetry_vdw_refined 0.271 r_nbd_other 0.254
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.326 r_dihedral_angle_1_deg 5.975 r_scbond_it 3.936 r_mcangle_it 2.596 r_angle_refined_deg 2.102 r_mcbond_it 1.495 r_angle_other_deg 1.006 r_symmetry_vdw_other 0.353 r_symmetry_vdw_refined 0.271 r_nbd_other 0.254 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.168 r_chiral_restr 0.138 r_nbtor_other 0.092 r_bond_refined_d 0.027 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 1847 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing