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Crystal structure of thermoacidophile-specific protein STK_08120 complexed with myristic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EJX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 23% (v/v) isopropanol, 0.2M ammonium acetate, 0.1M Tris-HCl, pH 8.0 , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.93 α = 90 b = 70.58 β = 90 c = 35.25 γ = 90
Symmetry Space Group P 21 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 77 CCD ADSC QUANTUM 210 2011-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.00000 Photon Factory BL-17A
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 1.8 50 13006 45.4
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 1.8 1.86 99.6 0.214 8.5 6.1
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 2EJX 1.8 20 12356 633 99.86 0.183 0.181 0.18 0.232 0.2302 RANDOM 18.58
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] 0.19 -0.28 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.031 r_dihedral_angle_3_deg 13.517 r_dihedral_angle_4_deg 13.438 r_dihedral_angle_1_deg 6.458 r_scangle_it 6.081 r_scbond_it 3.775 r_mcangle_it 2.156 r_angle_refined_deg 1.984 r_mcbond_it 1.233 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.031 r_dihedral_angle_3_deg 13.517 r_dihedral_angle_4_deg 13.438 r_dihedral_angle_1_deg 6.458 r_scangle_it 6.081 r_scbond_it 3.775 r_mcangle_it 2.156 r_angle_refined_deg 1.984 r_mcbond_it 1.233 r_chiral_restr 0.139 r_bond_refined_d 0.023 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1098 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 16
Software Software Software Name Purpose SERGUI data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling