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The crystal structure of glycogen phosphorylase in complex with (3R,4R,5R)-5-hydroxymethylpiperidine-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 2.47 50.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.636 α = 90 b = 128.636 β = 90 c = 116.455 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 95.8 0.076 9.5 5.5 51324 51324 -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 0.481 3.5 5.3 3850
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 48722 48722 2587 95.82 0.19557 0.19557 0.19347 0.23501 RANDOM 40.093
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] 0.89 0.89 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.248 r_dihedral_angle_4_deg 18.219 r_dihedral_angle_3_deg 17.098 r_dihedral_angle_1_deg 5.171 r_scangle_it 2.084 r_scbond_it 1.264 r_angle_refined_deg 1.088 r_mcangle_it 1.035 r_mcbond_it 0.597 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.248 r_dihedral_angle_4_deg 18.219 r_dihedral_angle_3_deg 17.098 r_dihedral_angle_1_deg 5.171 r_scangle_it 2.084 r_scbond_it 1.264 r_angle_refined_deg 1.088 r_mcangle_it 1.035 r_mcbond_it 0.597 r_nbtor_refined 0.304 r_nbd_refined 0.189 r_xyhbond_nbd_refined 0.124 r_symmetry_vdw_refined 0.113 r_symmetry_hbond_refined 0.109 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 6579 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling