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The crystal structure of glycogen phosphorylase in complex with (3R,4R,5R)-5-hydroxymethyl-1-(3-phenylpropyl)-piperidine-3,4-diol and phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HLF PDB ENTRY 1HLF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.7 287 BES, EDTA, pH 6.7, SMALL TUBES, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.46 50.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.522 α = 90 b = 128.522 β = 90 c = 116.437 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 MARRESEARCH 2005-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8063 EMBL/DESY, HAMBURG X13
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 90.91 98.4 0.065 14 5.4 52635 52635 -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 2.15 2.19 99.1 0.48 4.3 5.2 3829
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1HLF 2.15 90.91 49970 49970 2665 98.34 0.1914 0.1914 0.18994 0.21844 RANDOM 37.5
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] 0.67 0.67 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.544 r_dihedral_angle_4_deg 21.376 r_dihedral_angle_3_deg 16.241 r_dihedral_angle_1_deg 5.178 r_scangle_it 2.128 r_scbond_it 1.283 r_angle_refined_deg 1.074 r_mcangle_it 1.022 r_mcbond_it 0.588 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.544 r_dihedral_angle_4_deg 21.376 r_dihedral_angle_3_deg 16.241 r_dihedral_angle_1_deg 5.178 r_scangle_it 2.128 r_scbond_it 1.283 r_angle_refined_deg 1.074 r_mcangle_it 1.022 r_mcbond_it 0.588 r_nbtor_refined 0.304 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.14 r_xyhbond_nbd_refined 0.114 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6540 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling