☰ Navigation Tabs
The crystal structure of glycogen phosphorylase b in complex with (3R,4R,5R)-5-hydroxymethyl-1-(3-phenylpropyl)-piperidine-3,4-diol
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 2.45 49.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.356 α = 90 b = 128.356 β = 90 c = 116.257 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 2.07 90.91 99.2 0.054 16.9 5.4 59039 59039 -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 2.07 2.11 99 0.437 4.4 5.4 4265
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 2.07 90.91 56018 56018 2981 99.15 0.19004 0.19004 0.18849 0.21955 RANDOM 34.916
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] 0.79 0.79 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.068 r_dihedral_angle_4_deg 18.891 r_dihedral_angle_3_deg 15.601 r_dihedral_angle_1_deg 5.176 r_scangle_it 2.029 r_scbond_it 1.255 r_angle_refined_deg 1.039 r_mcangle_it 0.951 r_mcbond_it 0.553 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.068 r_dihedral_angle_4_deg 18.891 r_dihedral_angle_3_deg 15.601 r_dihedral_angle_1_deg 5.176 r_scangle_it 2.029 r_scbond_it 1.255 r_angle_refined_deg 1.039 r_mcangle_it 0.951 r_mcbond_it 0.553 r_nbtor_refined 0.303 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.153 r_xyhbond_nbd_refined 0.104 r_chiral_restr 0.075 r_symmetry_hbond_refined 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6604 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling