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activated diguanylate cyclase PleD in complex with c-di-GMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V0N PDB ENTRY 2V0N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 PROTEIN SOLUTION\: 100 MICROM PLED, 0.2 MM C-DI-GMP, 2 MM GMPCPP, 1 MM BECL2, 10 MM NAF, 10 MM MGCL2 RESERVOIR\: 0.1 M HEPES, PH 8.0, 0.73 M NA2SO4
Crystal Properties Matthews coefficient Solvent content 3.46 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.56 α = 90 b = 127.43 β = 90 c = 88.13 γ = 90
Symmetry Space Group P 21 21 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 MARRESEARCH 2006-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 72.48 87 0.1 5.6 3.45 42374 1.8
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 2.5 2.64 62.4 0.28 2.23 3.26
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 PDB ENTRY 2V0N 2.8 60 31368 1691 94.49 0.24053 0.23906 0.2395 0.26816 0.2647 RANDOM 11.413
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] -0.69 -1.28 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.452 r_dihedral_angle_4_deg 20.943 r_dihedral_angle_3_deg 16.815 r_dihedral_angle_1_deg 5.625 r_scangle_it 5.094 r_scbond_it 3.148 r_mcangle_it 1.772 r_angle_refined_deg 1.599 r_angle_other_deg 1.429 r_mcbond_it 0.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.452 r_dihedral_angle_4_deg 20.943 r_dihedral_angle_3_deg 16.815 r_dihedral_angle_1_deg 5.625 r_scangle_it 5.094 r_scbond_it 3.148 r_mcangle_it 1.772 r_angle_refined_deg 1.599 r_angle_other_deg 1.429 r_mcbond_it 0.955 r_chiral_restr 0.076 r_bond_refined_d 0.016 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6908 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 256
Software Software Software Name Purpose REFMAC refinement PHASER phasing