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Crystal structure of the CBS and DRTGG domains of the regulatory region of Clostridium perfringens pyrophosphatase complexed with activator, diadenosine tetraphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 25% PEG 4000, 100mM Tris/HCl pH 8.5, 200mM LiSO4, 0.25mM Ap4A, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.847 α = 90 b = 71.764 β = 90 c = 116.334 γ = 90
Symmetry Space Group P 21 21 21
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 Q315r 2008-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979260 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.27 20 98.8 0.053 0.053 19.78 7 24554 24554 -3 55.681
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) 2.31 2.44 95.5 0.374 0.374 4.6 6.9 3736
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 3L31 2.27 19.99 23255 1298 97.24 0.21123 0.20865 0.2134 0.25875 0.2551 RANDOM 45.19
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] 4.48 -1.22 -3.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.399 r_dihedral_angle_4_deg 20.855 r_dihedral_angle_3_deg 14.524 r_dihedral_angle_1_deg 5.995 r_scangle_it 3.193 r_scbond_it 2.042 r_mcangle_it 1.347 r_angle_refined_deg 1.341 r_angle_other_deg 1.219 r_mcbond_it 0.716
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.399 r_dihedral_angle_4_deg 20.855 r_dihedral_angle_3_deg 14.524 r_dihedral_angle_1_deg 5.995 r_scangle_it 3.193 r_scbond_it 2.042 r_mcangle_it 1.347 r_angle_refined_deg 1.341 r_angle_other_deg 1.219 r_mcbond_it 0.716 r_mcbond_other 0.133 r_chiral_restr 0.073 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3551 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 53
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction