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Crystal structure of glycogen phosphorylase b in complex with N-(-D-glucopyranosyl)-N'-(2-naphthyl)oxamides
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, pH6.7, SMALL TUBES, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.46 49.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.418 α = 90 b = 128.418 β = 90 c = 116.353 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 2006-01-01 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 30 99.5 0.056 17.1 5.3 65843 65843 -3 28.7
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 2.03 99.4 0.465 5.1 5.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1HLF 2 21.26 65793 62455 3338 99.5 0.19282 0.19156 0.1899 0.21649 0.2112 RANDOM 31.069
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] 0.65 0.65 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.076 r_dihedral_angle_4_deg 20.371 r_dihedral_angle_3_deg 15.08 r_dihedral_angle_1_deg 5.089 r_scangle_it 1.958 r_scbond_it 1.218 r_angle_refined_deg 1.031 r_mcangle_it 0.943 r_mcbond_it 0.552 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.076 r_dihedral_angle_4_deg 20.371 r_dihedral_angle_3_deg 15.08 r_dihedral_angle_1_deg 5.089 r_scangle_it 1.958 r_scbond_it 1.218 r_angle_refined_deg 1.031 r_mcangle_it 0.943 r_mcbond_it 0.552 r_nbtor_refined 0.304 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.15 r_symmetry_hbond_refined 0.132 r_xyhbond_nbd_refined 0.103 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 6637 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling