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Diguanylate cyclase DgcR (I-site mutant) in native state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V0N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291.15 0.2 M Magnesium sulfate, 20%PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.59 52.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.676 α = 90 b = 39.344 β = 108.77 c = 146.222 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS 2M-F 2017-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.979389 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 2.19 45.04 98.41 0.09907 0.1107 0.04849 0.998 10.7 5 38136 38.59
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 2.19 2.25 1.328 0.917 0.944 5
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 2V0N 2.2 30 35759 1797 98.47 0.2282 0.2266 0.2292 0.2591 0.2628 RANDOM 62.313
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 35.451 r_dihedral_angle_4_deg 19.992 r_dihedral_angle_3_deg 18.014 r_dihedral_angle_1_deg 6.923 r_angle_refined_deg 1.661 r_angle_other_deg 1.271 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.451 r_dihedral_angle_4_deg 19.992 r_dihedral_angle_3_deg 18.014 r_dihedral_angle_1_deg 6.923 r_angle_refined_deg 1.661 r_angle_other_deg 1.271 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4672 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction Aimless data scaling PHASER phasing