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Crystal structure of putative UDP-N-acetylglucosamine pyrophosphorylase from Entamoeba histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JV1 1jv1 molecule A residues 68-407
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 96.3 mg/mL of EnhiA.01126.b.A1 PS00631 3C cleaved against JCSG+ condition H9, 0.2 M lithium sulfate, 0.1 M BisTris pH 5.5, 25% PEG 3350 with 15% ethylene glycol as cryo-protectant, crystal tracking ID 216241h9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.77 55.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.52 α = 90 b = 77.54 β = 90 c = 86.87 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 CCD ADSC QUANTUM 315r 2010-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97946 ALS 5.0.3
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 1.8 50 100 0.046 30.45 9.7 48592 48589 -3 32.461
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 1.8 1.85 100 0.529 4.4
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 1jv1 molecule A residues 68-407 1.8 50 48468 2450 99.75 0.1909 0.189 0.1903 0.2266 0.2319 RANDOM 31.9097
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] -0.07 -0.45 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.68 r_dihedral_angle_4_deg 15.189 r_dihedral_angle_3_deg 12.158 r_dihedral_angle_1_deg 5.786 r_scangle_it 3.336 r_scbond_it 1.949 r_angle_refined_deg 1.3 r_mcangle_it 1.294 r_mcbond_it 0.701 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.68 r_dihedral_angle_4_deg 15.189 r_dihedral_angle_3_deg 12.158 r_dihedral_angle_1_deg 5.786 r_scangle_it 3.336 r_scbond_it 1.949 r_angle_refined_deg 1.3 r_mcangle_it 1.294 r_mcbond_it 0.701 r_chiral_restr 0.098 r_bond_refined_d 0.018 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3199 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 9
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction