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Crystal structure of a HTH XRE-family like protein from Agrobacterium tumefaciens
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 2M Ammonium sulfate, 0.2M K/Na tartrate, 0.1M Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.42 64.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.696 α = 90 b = 70.696 β = 90 c = 103.736 γ = 120
Symmetry Space Group P 64 2 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 ADSC QUANTUM 315 2006-02-05 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97948, 0.97935 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 35.35 97.5 0.049 11.9 10649 10649 -3 38.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.05 81.3 0.347 2 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 MAD THROUGHOUT 2 35.35 -3 10139 10139 509 97.53 0.19831 0.19831 0.19607 0.1953 0.24382 0.229 RANDOM 65.677
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] 0.9 0.45 0.9 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.974 r_dihedral_angle_4_deg 17.649 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_1_deg 4.268 r_scangle_it 3.856 r_scbond_it 2.356 r_angle_refined_deg 1.45 r_mcangle_it 1.312 r_mcbond_it 0.834 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.974 r_dihedral_angle_4_deg 17.649 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_1_deg 4.268 r_scangle_it 3.856 r_scbond_it 2.356 r_angle_refined_deg 1.45 r_mcangle_it 1.312 r_mcbond_it 0.834 r_nbtor_refined 0.307 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.184 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.112 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 501 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building