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Diguanylate cyclase domain of DgcZ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W25 PDB ENTRY 1W25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 293 100mM Tris, 22.5% PEG 4000, pH 8.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.623 α = 90 b = 79.623 β = 90 c = 51.207 γ = 120
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 MARMOSAIC 225 mm CCD 2011-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 51.21 100 0.075 0.075 24.1 12.5 17292 19.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 100 0.346 0.346 7.6 12
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1W25 1.8 15 17232 17232 872 100 0.167 0.166 0.1723 0.201 0.2076 RANDOM 19.5
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] -0.21 -0.11 -0.21 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.862 r_dihedral_angle_4_deg 13.563 r_dihedral_angle_3_deg 11.863 r_scangle_it 6.019 r_dihedral_angle_1_deg 5.523 r_scbond_it 4.094 r_mcangle_it 2.894 r_mcbond_it 1.815 r_angle_refined_deg 1.281 r_angle_other_deg 0.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.862 r_dihedral_angle_4_deg 13.563 r_dihedral_angle_3_deg 11.863 r_scangle_it 6.019 r_dihedral_angle_1_deg 5.523 r_scbond_it 4.094 r_mcangle_it 2.894 r_mcbond_it 1.815 r_angle_refined_deg 1.281 r_angle_other_deg 0.804 r_mcbond_other 0.681 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1370 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing