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Crystal structure of N-terminal GTP-binding domain of EngA from Thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MKY PDB ENTRY 1MKY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M MES pH 6.0, 1.0M Pottasium sodium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.421 α = 119.88 b = 50.539 β = 90.02 c = 50.453 γ = 88.91
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD RIGAKU JUPITER 210 2006-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0000 SPring-8 BL26B2
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 1.96 43.9 92 0.048 14.9 1.91 20112 -3 11.3
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 1.96 2.02 78.6 0.177 2.56 1.7 1713
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 1MKY 1.96 43.81 20112 976 92.4 0.195 0.195 0.1932 0.225 0.2224 RANDOM 22
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] -1.58 -2.02 -0.56 3.31 2.83 -1.73
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 4.9 c_scbond_it 3.32 c_mcangle_it 2.85 c_improper_angle_d 2.37 c_mcbond_it 2 c_angle_deg 1.5 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 4.9 c_scbond_it 3.32 c_mcangle_it 2.85 c_improper_angle_d 2.37 c_mcbond_it 2 c_angle_deg 1.5 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2386 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 56
Software Software Software Name Purpose CNS refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing