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Crystal structure of YoeB under PEG condition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A6Q extracted from YoeB structure from 2A6Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.2 Tris-HCl, MgCl, PEG8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K
Crystal Properties Matthews coefficient Solvent content 2.3 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.898 α = 90 b = 43.138 β = 118.49 c = 89.367 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 100 CCD ADSC QUANTUM 315 Collimating and Focusing mirrors 2004-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A
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 2.05 44.72 99.58 19.99 3.6 34800 34757 24.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.05 2.12 95.1 95.1 3.3 3270
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 extracted from YoeB structure from 2A6Q 2.05 14.98 2 34700 34242 1719 98.4 0.2 0.198 0.196 0.1995 0.229 0.1915 random 30.43
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] 2.38 -1.77 -4.11 1.73
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.8 c_scangle_it 3.494 c_mcangle_it 2.44 c_scbond_it 2.296 c_mcbond_it 1.517 c_angle_deg 1.2 c_improper_angle_d 0.63 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4325 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction HKL-2000 data reduction CCP4 data scaling CNS phasing