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Response regulator PleD in complex with c-diGMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.2 CRYSTALS WERE OBTAINED AT ROOM TEMPERATURE BY HANGING DROP VAPOUR DIFFUSION. FOR THIS, PLED AT A NOMINAL CONCENTRATION OF 10 MG/ML IN 20 MM TRIS-HCL (PH 8.0), 100 MM NACL, 1 MM DTT, 2 MM MGCL2 AND 0.8 MM C-DIGMP6 WAS MIXED WITH THE RESERVOIR (1.0 M GLYCINE PH 9.2, 2 % DIOXANE, 14.5 % POLYETHYLENE GLYCOL 20K) AT A RATIO 1 TO 1.
Crystal Properties Matthews coefficient Solvent content 3.9 69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.87 α = 90 b = 135.87 β = 90 c = 169.247 γ = 90
Symmetry Space Group P 42 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 2003-12-14 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 2.7 60.86 99.3 0.08 16.42 5.7 43706 -3.7
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 2.7 2.72 98.7 0.36 2.96 5.48
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.7 50 41469 2202 98.9 0.212 0.21 0.2184 0.239 RANDOM 25.61
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] -0.07 -0.07 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.956 r_dihedral_angle_4_deg 16.945 r_dihedral_angle_3_deg 16.4 r_dihedral_angle_1_deg 5.586 r_scangle_it 3.706 r_scbond_it 2.416 r_mcangle_it 1.307 r_angle_refined_deg 1.211 r_mcbond_it 1.129 r_angle_other_deg 0.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.956 r_dihedral_angle_4_deg 16.945 r_dihedral_angle_3_deg 16.4 r_dihedral_angle_1_deg 5.586 r_scangle_it 3.706 r_scbond_it 2.416 r_mcangle_it 1.307 r_angle_refined_deg 1.211 r_mcbond_it 1.129 r_angle_other_deg 0.773 r_symmetry_vdw_other 0.295 r_nbd_refined 0.201 r_mcbond_other 0.18 r_symmetry_vdw_refined 0.177 r_nbd_other 0.17 r_xyhbond_nbd_refined 0.108 r_nbtor_other 0.083 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 6962 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 233
Software Software Software Name Purpose DM model building TRUNCATE data scaling SHELXD phasing SHARP phasing SOLOMON phasing DM phasing REFMAC refinement