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Crystal structure of response regulator protein TrrA (TM1360) from Thermotoga maritima in complex with Mg(2+)-BeF (wild type)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9.5 293 40% PEG600, 0.1 M CHES, pH 9.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.978 α = 90 b = 32.978 β = 90 c = 196.968 γ = 90
Symmetry Space Group P 41 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 100 CCD RIGAKU JUPITER 210 2005-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.66 50 98 0.046 31.6 4.1 13692 -3 16.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.66 1.72 94 0.111 6.9 3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3A10 1.66 20 13625 685 98.49 0.191 0.189 0.24 0.2396 RANDOM 16.163
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] -0.04 -0.04 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.118 r_dihedral_angle_4_deg 16.207 r_dihedral_angle_3_deg 11.567 r_dihedral_angle_1_deg 5.937 r_scangle_it 4.17 r_scbond_it 2.622 r_angle_refined_deg 1.591 r_mcangle_it 1.568 r_mcbond_it 1.023 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.118 r_dihedral_angle_4_deg 16.207 r_dihedral_angle_3_deg 11.567 r_dihedral_angle_1_deg 5.937 r_scangle_it 4.17 r_scbond_it 2.622 r_angle_refined_deg 1.591 r_mcangle_it 1.568 r_mcbond_it 1.023 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.15 r_metal_ion_refined 0.105 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 966 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing