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Diguanylate cyclase DgcR (I-site mutant) in activated state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZXB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 0.06 M Divalents, 0.1M Buffer System 1 pH 6.5, 50%v/v Precipitant Mix 2 (Morpheus I A2).
Divalents: 0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dehydrate.
Buffer System 1: 1.0M Imidazole; MES monohydrate (acid), pH 6.5.
Precipitant Mix 2: EDO_P8K, 40% v/v Ethylene glycol, 20 % w/v PEG 8000.
Crystal Properties Matthews coefficient Solvent content 2.37 48.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.812 α = 90 b = 247.368 β = 90 c = 41.539 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 93.15 PIXEL DECTRIS PILATUS 2M-F 2017-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.7 45.26 95.6 0.144 0.177 0.101 0.991 6.3 4.3 36666
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.82 93.1 0.901 0.649 0.513 1.6 4.2
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 6ZXB 2.8 30 35759 1599 93.66 0.2282 0.23658 0.2273 0.28813 0.2779 RANDOM 66.792
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] 1.55 -0.43 -3.1 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.442 r_dihedral_angle_4_deg 18.974 r_dihedral_angle_3_deg 17.721 r_dihedral_angle_1_deg 6.927 r_angle_refined_deg 1.861 r_angle_other_deg 1.271 r_chiral_restr 0.129 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.442 r_dihedral_angle_4_deg 18.974 r_dihedral_angle_3_deg 17.721 r_dihedral_angle_1_deg 6.927 r_angle_refined_deg 1.861 r_angle_other_deg 1.271 r_chiral_restr 0.129 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9360 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing