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Crystal structure of 1-(beta-D-glucopyranosyl)-4-substituted-1,2,3-triazoles in complex with glycogen phosphorylase
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 6.8 289 pH 6.8, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.47 50.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.791 α = 90 b = 128.791 β = 90 c = 116.188 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 100 CCD MARRESEARCH 2007-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.80880 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 30 99 0.091 19.9 5.3 43536 30.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.34 98.6 0.501 3.9 5.3 2120
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2PRJ 2.3 30 41320 2193 98.88 0.17612 0.17427 0.1732 0.21049 0.2099 RANDOM 27.978
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] 0.57 0.57 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.788 r_dihedral_angle_4_deg 19.253 r_dihedral_angle_3_deg 16.075 r_dihedral_angle_1_deg 5.401 r_scangle_it 2.099 r_scbond_it 1.254 r_angle_refined_deg 1.085 r_mcangle_it 0.953 r_mcbond_it 0.534 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.788 r_dihedral_angle_4_deg 19.253 r_dihedral_angle_3_deg 16.075 r_dihedral_angle_1_deg 5.401 r_scangle_it 2.099 r_scbond_it 1.254 r_angle_refined_deg 1.085 r_mcangle_it 0.953 r_mcbond_it 0.534 r_nbtor_refined 0.302 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.081 r_symmetry_hbond_refined 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6604 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 26
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling