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Glycogen Phosphorylase complex with 1(-D-ribofuranosyl) cyanuric acid
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 10mM Bes buffer, 3mM DDT, pH6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.47 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.62 α = 90 b = 128.62 β = 90 c = 116.379 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 298 CCD MAR CCD 165 mm 2005-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.81 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 98.5 0.047 18.6 4.9 65282 65282 -3
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) 2 2.03 98.1 0.435 4.5 4.9
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2PRJ 2 21.58 61937 3311 98.48 0.19092 0.19015 0.1895 0.20515 0.2051 RANDOM 34.177
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] 0.85 0.85 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.959 r_dihedral_angle_4_deg 17.531 r_dihedral_angle_3_deg 15.174 r_dihedral_angle_1_deg 5.025 r_scangle_it 1.969 r_scbond_it 1.205 r_angle_refined_deg 1.023 r_mcangle_it 0.941 r_mcbond_it 0.547 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.959 r_dihedral_angle_4_deg 17.531 r_dihedral_angle_3_deg 15.174 r_dihedral_angle_1_deg 5.025 r_scangle_it 1.969 r_scbond_it 1.205 r_angle_refined_deg 1.023 r_mcangle_it 0.941 r_mcbond_it 0.547 r_nbtor_refined 0.302 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.101 r_chiral_restr 0.074 r_symmetry_hbond_refined 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6638 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling