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Crystal structure of Glycogen Debranching Enzyme GlgX from Escherichia coli K-12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VR5 PDB ENTRY 2VR5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 MPD 47%, NA-CITRATE 0.2M, PEG 3350 4%, HEPES PH8.0, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.34 46.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.852 α = 90 b = 91.937 β = 90 c = 97.596 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC CCD 2008-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A PAL/PLS 4A
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 2.25 30 90.8 0.15 6.5 12.3 30337 16.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.33 96.9 0.24 3.4 8.7
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 2VR5 2.25 29.96 30337 1495 90.8 0.209 0.209 0.2077 0.265 0.2643 RANDOM 29.6
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] -9.53 -11.27 20.8
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.9 c_scangle_it 2.6 c_scbond_it 1.82 c_mcangle_it 1.77 c_angle_deg 1.4 c_mcbond_it 1.12 c_improper_angle_d 0.86 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.9 c_scangle_it 2.6 c_scbond_it 1.82 c_mcangle_it 1.77 c_angle_deg 1.4 c_mcbond_it 1.12 c_improper_angle_d 0.86 c_bond_d 0.006 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 5179 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 5
Software Software Software Name Purpose CNS refinement PHASER phasing