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The crystal structure of glycogen phosphorylase b in complex with 2,5-dihydroxy-4-(beta-D-glucopyranosyl)-chlorobenzene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRJ PDB ENTRY 2PRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.7 289 10 mM BES Buffer, 3 mM DTT, 1 mM IMP, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.45 α = 90 b = 128.45 β = 90 c = 116.364 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 CCD MAR CCD 165 mm 2005-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8156 EMBL/DESY, HAMBURG X11
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 30 93.9 0.065 21.2 5.4 65452 64845 -3 31.1
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 2.03 90.9 0.398 5.2 5.4 3213
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 (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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2PRJ 2 30 65452 62101 3308 99 0.19105 0.19105 0.19005 0.1909 0.20947 0.2084 RANDOM 35.178
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] 0.93 0.93 -1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.526 r_dihedral_angle_4_deg 19.475 r_dihedral_angle_3_deg 15.234 r_dihedral_angle_1_deg 5.109 r_scangle_it 2.055 r_scbond_it 1.263 r_angle_refined_deg 1.028 r_mcangle_it 0.954 r_mcbond_it 0.56 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.526 r_dihedral_angle_4_deg 19.475 r_dihedral_angle_3_deg 15.234 r_dihedral_angle_1_deg 5.109 r_scangle_it 2.055 r_scbond_it 1.263 r_angle_refined_deg 1.028 r_mcangle_it 0.954 r_mcbond_it 0.56 r_nbtor_refined 0.302 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.098 r_chiral_restr 0.073 r_symmetry_hbond_refined 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6604 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 20
Software Software Software Name Purpose DNA data collection REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing