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Crystal structure of GenX from Escherichia coli in complex with lysyladenylate analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LYL PDB entry 1LYL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 PEG 4000, Hepes-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.8 α = 95.47 b = 69.15 β = 106.51 c = 94.08 γ = 90.46
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 ADSC QUANTUM 315 2006-05-19 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.9 50 95.4 0.086 99019 15.2
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 1.9 1.97 77.9 0.278
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 1LYL 1.9 44.87 99017 9925 95.2 0.171 0.171 0.1706 0.219 0.2186 RANDOM 28.4
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] -3.75 -3.62 0.19 6.73 -4.37 -2.99
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 7.6 c_scbond_it 5.98 c_mcangle_it 4.59 c_mcbond_it 3.86 c_angle_deg 1.5 c_improper_angle_d 0.92 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9876 Nucleic Acid Atoms Solvent Atoms 1031 Heterogen Atoms 128
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing CNS refinement HKL-2000 data reduction SCALEPACK data scaling