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Crystal structure of the diguanylate cyclase DgcZ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T90 PDB ENTRIES 3T90 AND 3TVK experimental model PDB 3TVK PDB ENTRIES 3T90 AND 3TVK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 200 mM calcium acetate, 20.0% PEG4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.81 56.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.593 α = 90 b = 102.593 β = 90 c = 129.156 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 2011-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.9 89 99.9 7096 7076 104.93
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 3.9 4.11 99.87 0.77 0.83 1 7.93
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 ENTRIES 3T90 AND 3TVK 3.9 73.2 7096 7072 335 99.76 0.2421 0.2422 0.2428 0.2411 0.256 RANDOM 68.05
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] -21.3747 -21.3747 42.7495
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.6 t_omega_torsion 4.69 t_angle_deg 1.04 t_bond_d 0.016 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.6 t_omega_torsion 4.69 t_angle_deg 1.04 t_bond_d 0.016 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4348 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MARMOSAIC data collection MOSFLM data reduction SCALA data scaling PHASER phasing BUSTER refinement