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Glycogen Phosphorylase in complex with N-4-chlorobenzoyl-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 50.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.841 α = 90 b = 128.841 β = 90 c = 116.486 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 2006-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.912 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 1.95 99 97.9 0.046 20.1 5.2 70275 70275 -3 25
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) 1.95 1.99 93.1 0.318 4.3 5.3 3280
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 pdb entry 2PRJ 1.96 91.29 66980 66980 3563 99.82 0.1858 0.18469 0.2064 RANDOM 27.235
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] 0.63 0.63 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.119 r_dihedral_angle_4_deg 19.562 r_dihedral_angle_3_deg 14.679 r_dihedral_angle_1_deg 5.096 r_scangle_it 1.931 r_scbond_it 1.205 r_angle_refined_deg 1.011 r_mcangle_it 0.901 r_mcbond_it 0.536 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.119 r_dihedral_angle_4_deg 19.562 r_dihedral_angle_3_deg 14.679 r_dihedral_angle_1_deg 5.096 r_scangle_it 1.931 r_scbond_it 1.205 r_angle_refined_deg 1.011 r_mcangle_it 0.901 r_mcbond_it 0.536 r_nbtor_refined 0.301 r_nbd_refined 0.175 r_symmetry_vdw_refined 0.139 r_symmetry_hbond_refined 0.116 r_xyhbond_nbd_refined 0.095 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 6632 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling