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PaMucR Phosphodiesterase, c-di-GMP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 0.055M MES, 0.045M Imidazole, 12.5% PEG 1000, 12.5% PEG3350, 12.5% MPD, 0.03M diethyleneglycol, 0.03M triethyleneglycol, 0.03M tetraethyleneglycol, 0.03M pentaethyleneglycol
Crystal Properties Matthews coefficient Solvent content 2.23 44.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.37 α = 90 b = 116.11 β = 102.52 c = 52.14 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 45.27 99.9 0.167 0.994 11.3 6.9 24883
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.27 2.33 99.8 0.677 0.853 2.9 6.9
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 2R6O 2.27 45.27 23617 1249 99.92 0.1975 0.19527 0.2033 0.23821 0.2406 RANDOM 35.452
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] -0.73 0.52 -0.21 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.947 r_dihedral_angle_4_deg 17.879 r_dihedral_angle_3_deg 12.888 r_dihedral_angle_1_deg 5.446 r_long_range_B_refined 4.073 r_long_range_B_other 4.041 r_scangle_other 1.797 r_mcangle_it 1.661 r_mcangle_other 1.66 r_angle_refined_deg 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.947 r_dihedral_angle_4_deg 17.879 r_dihedral_angle_3_deg 12.888 r_dihedral_angle_1_deg 5.446 r_long_range_B_refined 4.073 r_long_range_B_other 4.041 r_scangle_other 1.797 r_mcangle_it 1.661 r_mcangle_other 1.66 r_angle_refined_deg 1.44 r_scbond_it 1.064 r_scbond_other 1.059 r_mcbond_it 0.976 r_mcbond_other 0.975 r_angle_other_deg 0.71 r_chiral_restr 0.068 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3563 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing