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Crystal structure of the uridine diphosphate N-acetylglucosamine pyrophosphorylase from Trypanosoma brucei in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JV1 PDB ENTRY 1JV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 25% PEG3350, 0.2M (NH4)2SO4, 0.1 M BIS-TRIS PH5.5
Crystal Properties Matthews coefficient Solvent content 2.38 48.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.93 α = 90 b = 103 β = 90 c = 187.14 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
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 1.75 25 99.7 0.07 13.6 5.7 58590
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) 1 1.75 25 99.2 0.35 4.5 5.4
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 1JV1 1.75 40 57345 1194 99.67 0.18986 0.18923 0.1879 0.22101 0.2189 RANDOM 19.519
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] -0.27 0.55 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.05 r_dihedral_angle_4_deg 17.311 r_dihedral_angle_3_deg 13.428 r_dihedral_angle_1_deg 5.369 r_angle_refined_deg 1.306 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.05 r_dihedral_angle_4_deg 17.311 r_dihedral_angle_3_deg 13.428 r_dihedral_angle_1_deg 5.369 r_angle_refined_deg 1.306 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4047 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALEPACK data scaling BALBES phasing