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Glycogen Phosphorylase b in complex with N-benzoyl-N'-beta-D-glucopyranosyl urea
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, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.48 50.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.653 α = 90 b = 128.653 β = 90 c = 116.75 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 ADSC QUANTUM 4 2001-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.87 SRS PX9.6
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 1.8 30 97.7 0.038 15.63 4.9 88811 88811 -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) 1.8 1.83 95 0.481 1.94 4.2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT pdb entry 2PRJ 1.8 30 84369 4448 97.61 0.1996 0.19853 0.22025 RANDOM 28.684
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] 0.71 0.71 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.101 r_dihedral_angle_4_deg 18.738 r_dihedral_angle_3_deg 15.627 r_dihedral_angle_1_deg 5.01 r_scangle_it 1.896 r_scbond_it 1.171 r_angle_refined_deg 1.025 r_mcangle_it 0.856 r_mcbond_it 0.499 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.101 r_dihedral_angle_4_deg 18.738 r_dihedral_angle_3_deg 15.627 r_dihedral_angle_1_deg 5.01 r_scangle_it 1.896 r_scbond_it 1.171 r_angle_refined_deg 1.025 r_mcangle_it 0.856 r_mcbond_it 0.499 r_nbtor_refined 0.302 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.116 r_symmetry_hbond_refined 0.086 r_xyhbond_nbd_refined 0.085 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6613 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling