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Glycogen Phosphorylase complex with 1(-D-glucopyranosyl) uracil
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 50.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.577 α = 90 b = 128.577 β = 90 c = 116.517 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 2005-09-28 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 98.7 0.042 22 4.9 65496 65496 -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) 1 2 2.05 98.3 0.445 4.1 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 21.6 62139 3317 98.74 0.19649 0.1952 0.1921 0.22063 0.2176 RANDOM 34.366
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] 0.86 0.86 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.754 r_dihedral_angle_4_deg 18.994 r_dihedral_angle_3_deg 15.359 r_dihedral_angle_1_deg 5.063 r_scangle_it 2.084 r_scbond_it 1.275 r_angle_refined_deg 1.036 r_mcangle_it 0.958 r_mcbond_it 0.554 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.754 r_dihedral_angle_4_deg 18.994 r_dihedral_angle_3_deg 15.359 r_dihedral_angle_1_deg 5.063 r_scangle_it 2.084 r_scbond_it 1.275 r_angle_refined_deg 1.036 r_mcangle_it 0.958 r_mcbond_it 0.554 r_nbtor_refined 0.303 r_nbd_refined 0.183 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.108 r_chiral_restr 0.073 r_symmetry_hbond_refined 0.051 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 257 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling