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Glycogen Phosphorylase b in complex with N-4-phenylbenzoyl-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 50.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.763 α = 90 b = 128.763 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 MAR CCD 165 mm 2004-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.813 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 2.15 30 99.8 0.071 18.1 7.4 53808 53808 -3 27.3
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) 2.15 2.19 99.6 0.367 6.2 7.6 2632
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 2.15 30 51023 2729 99.78 0.18223 0.18077 0.20947 RANDOM 26.805
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] 0.56 0.56 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.057 r_dihedral_angle_4_deg 19.528 r_dihedral_angle_3_deg 15.041 r_dihedral_angle_1_deg 5.187 r_scangle_it 1.982 r_scbond_it 1.21 r_angle_refined_deg 1.043 r_mcangle_it 0.93 r_mcbond_it 0.549 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.057 r_dihedral_angle_4_deg 19.528 r_dihedral_angle_3_deg 15.041 r_dihedral_angle_1_deg 5.187 r_scangle_it 1.982 r_scbond_it 1.21 r_angle_refined_deg 1.043 r_mcangle_it 0.93 r_mcbond_it 0.549 r_nbtor_refined 0.302 r_nbd_refined 0.178 r_symmetry_hbond_refined 0.128 r_symmetry_vdw_refined 0.126 r_xyhbond_nbd_refined 0.103 r_chiral_restr 0.076 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 271 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling