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Crystal structure of the C-terminal fragment of AAA+ATPase from Haemophilus influenzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R9G PDB entry 2R9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1M tri-Sodium citrate pH 5.6, 2M Ammonium sulfate, 0.2M Potassium sodium tartrate tetrahydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.99 38.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.085 α = 90 b = 93.085 β = 90 c = 83.413 γ = 90
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 MAR CCD 165 mm 2007-08-20 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2007-08-16 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID 2 SYNCHROTRON NSLS BEAMLINE X29A 0.9793 NSLS X29A
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 1.85 23.12 99.4 0.079 4.8 3.1 30371 30371
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 1.85 1.93 100 0.44 0.38 2.2 3.1 7540
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 (All) 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 SAD THROUGHOUT PDB entry 2R9G 1.85 23.12 29276 29276 1468 96.41 0.189 0.189 0.187 0.1872 0.24 0.2381 RANDOM 24.288
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] -0.54 -0.54 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.249 r_dihedral_angle_4_deg 17.124 r_dihedral_angle_3_deg 15.639 r_scangle_it 6.62 r_dihedral_angle_1_deg 5.309 r_scbond_it 4.597 r_mcangle_it 2.696 r_mcbond_it 1.835 r_angle_refined_deg 1.349 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.249 r_dihedral_angle_4_deg 17.124 r_dihedral_angle_3_deg 15.639 r_scangle_it 6.62 r_dihedral_angle_1_deg 5.309 r_scbond_it 4.597 r_mcangle_it 2.696 r_mcbond_it 1.835 r_angle_refined_deg 1.349 r_nbtor_refined 0.321 r_nbd_refined 0.235 r_symmetry_hbond_refined 0.225 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.199 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2578 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 15
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction PHASER phasing