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Crystal structure of glycogen phosphorylase b in complex with C-(1-acetamido-alpha-D-glucopyranosyl) formamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.7 289 BES, EDTA, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.43 49.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.98 α = 90 b = 127.98 β = 90 c = 115.529 γ = 90
Symmetry Space Group P 43 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 293 IMAGE PLATE MARRESEARCH 2003-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8015 EMBL/DESY, HAMBURG X13
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 2.06 30 99.4 0.083 17.1 6.6 59423 59423 -3 28.1
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 2.06 2.1 92.8 0.565 2.9 4.3 2723
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1GFZ 2.06 29.98 59538 59358 3004 99.3 0.185 0.185 0.205 RANDOM 33.9
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] 3.42 3.42 -6.83
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 3.2 c_scbond_it 2.06 c_mcangle_it 1.98 c_angle_deg 1.3 c_mcbond_it 1.23 c_improper_angle_d 0.78 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6585 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 38
Software Software Software Name Purpose CNS refinement MAR345 data collection SCALEPACK data scaling CNS phasing