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Crystal structure of the CBS-domain containing protein ATU1752 from Agrobacterium tumefaciens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RC3 model of protein made from 3rc3 using MrBUMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 0.1 M Tris 8.0, 0.2 M LiSO4, 30% PEG 4K plus 0.015 mg/ml V8 protease. Cryoprotected with Paratone-N oil, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.19 43.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.247 α = 115.21 b = 58.075 β = 106.15 c = 59.056 γ = 94.94
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 SBC-2 mirrors 2008-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-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 2.4 30.37 81.7 0.067 18.55 4.5 24264 19824 47.9
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 2.4 2.44 11.6 0.545 1.1 2.1 143
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 model of protein made from 3rc3 using MrBUMP 2.7 30.37 14238 783 91.56 0.19887 0.19536 0.2284 0.26164 0.2778 RANDOM 33.886
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] 0.05 -0.03 0.02 0.02 -0.08 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.903 r_dihedral_angle_4_deg 24.07 r_dihedral_angle_3_deg 22.661 r_dihedral_angle_1_deg 6.697 r_angle_refined_deg 2.251 r_symmetry_vdw_refined 0.342 r_nbtor_refined 0.313 r_nbd_refined 0.237 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.903 r_dihedral_angle_4_deg 24.07 r_dihedral_angle_3_deg 22.661 r_dihedral_angle_1_deg 6.697 r_angle_refined_deg 2.251 r_symmetry_vdw_refined 0.342 r_nbtor_refined 0.313 r_nbd_refined 0.237 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.146 r_bond_refined_d 0.021 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3829 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 288
Software Software Software Name Purpose HKL-3000 data collection MrBUMP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling