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Crystal structure of propionate catabolism operon regulatory protein prpR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1M Hepes pH 7.5, 15% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.657 α = 85.03 b = 58.545 β = 88.56 c = 103.576 γ = 86.94
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 QUANTUM 315 2007-02-28 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MAR CCD 165 mm 2007-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9793 NSLS X29A 2 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 2.1 50 97.9 0.089 7.2 2.5 47669 47669
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) 2.1 2.18 97.3 0.313 0.296 1.9 2.4 4671
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 37.06 47666 47666 2436 97.82 0.204 0.204 0.201 0.2294 0.252 0.2703 RANDOM 39.91
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] -0.64 -0.18 -0.41 1.34 0.44 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.498 r_dihedral_angle_4_deg 20.812 r_dihedral_angle_3_deg 17.19 r_dihedral_angle_1_deg 5.669 r_scangle_it 3.126 r_scbond_it 2.021 r_angle_refined_deg 1.36 r_mcangle_it 1.242 r_mcbond_it 0.782 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.498 r_dihedral_angle_4_deg 20.812 r_dihedral_angle_3_deg 17.19 r_dihedral_angle_1_deg 5.669 r_scangle_it 3.126 r_scbond_it 2.021 r_angle_refined_deg 1.36 r_mcangle_it 1.242 r_mcbond_it 0.782 r_nbtor_refined 0.3 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.174 r_symmetry_hbond_refined 0.142 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5946 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction HKL2Map phasing