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Crystal Structure of GGDEF domain from T.maritima (active-like dimer)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ICL PDB ENTRY 3ICL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 0.15 M LITHIUM SULFATE, 0.1 M CITRIC ACID (PH 4.0), 10% (W/V) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.28 46.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.89 α = 90 b = 52.12 β = 124.05 c = 73.71 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 291 PIXEL DECTRIS PILATUS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 36.49 100 0.12 11.4 6.8 27197 5 21.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 100 0.32 5.9 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 PDB ENTRY 3ICL 1.9 22.71 27172 1362 99.97 0.2091 0.2073 0.2154 0.2413 0.2496 RANDOM 25.07
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] 0.8675 -0.1773 -0.1205 -0.7469
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.44 t_omega_torsion 3.05 t_angle_deg 1.03 t_bond_d 0.01 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 17.44 t_omega_torsion 3.05 t_angle_deg 1.03 t_bond_d 0.01 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 2508 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 92
Software Software Software Name Purpose BUSTER refinement MOSFLM data reduction SCALA data scaling BALBES phasing