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Crystal structure of YagE, a prophage protein from E. coli K12 in complex with KDGal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 298 100mM HEPES pH 6.5, 200mM MgCl2, 25% PEG 3350, 50mM PYRUVATE, 50mM GLYCERALDEHYDE, Microbatch, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.39 48.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.86 α = 90 b = 155.13 β = 90 c = 55.71 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 100 2010-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95374 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.19 49.18 99.1 0.125 14.01 63549 -3 28.753
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.19 2.25 92.4 0.444 0.47 5.4
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 2V8Z 2.19 49.18 63549 3178 100 0.199 0.197 0.1953 0.237 0.2332 RANDOM 20.613
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] -1.72 2.58 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.714 r_dihedral_angle_4_deg 17.645 r_dihedral_angle_3_deg 15.177 r_dihedral_angle_1_deg 6.153 r_scangle_it 4.722 r_scbond_it 3.092 r_angle_refined_deg 1.868 r_mcangle_it 1.582 r_mcbond_it 0.878 r_chiral_restr 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.714 r_dihedral_angle_4_deg 17.645 r_dihedral_angle_3_deg 15.177 r_dihedral_angle_1_deg 6.153 r_scangle_it 4.722 r_scbond_it 3.092 r_angle_refined_deg 1.868 r_mcangle_it 1.582 r_mcbond_it 0.878 r_chiral_restr 0.145 r_bond_refined_d 0.024 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9024 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 76
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction