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Crystal Structure of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphorylase in complex with UTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YQS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2M sodium formate and 20% peg 3350
Crystal Properties Matthews coefficient Solvent content 2.56 51.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.711 α = 90 b = 139.98 β = 90 c = 146.293 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 2M 2007-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.9 ESRF ID23-2
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 2.4 20 99 0.086 13 3.8 46020
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 2.4 2.49 0.325
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 2YQS 2.4 20 45031 942 99.09 0.22849 0.22743 0.2257 0.27888 0.2769 RANDOM 34.841
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] 1 -2.39 1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.057 r_dihedral_angle_3_deg 15.592 r_dihedral_angle_4_deg 13.917 r_dihedral_angle_1_deg 5.777 r_scangle_it 1.938 r_scbond_it 1.228 r_angle_refined_deg 1.227 r_mcangle_it 0.957 r_mcbond_it 0.56 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.057 r_dihedral_angle_3_deg 15.592 r_dihedral_angle_4_deg 13.917 r_dihedral_angle_1_deg 5.777 r_scangle_it 1.938 r_scbond_it 1.228 r_angle_refined_deg 1.227 r_mcangle_it 0.957 r_mcbond_it 0.56 r_nbtor_refined 0.301 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.181 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 7288 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing