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Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans, in the product-binding form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YQC PDB ENTRY 2YQC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 20% PEG 6000, 0.1M ammonium sulfate, 15% glycerol, 0.01M uridine-N-acetylglucosamine, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.44 49.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.947 α = 90 b = 90.868 β = 90 c = 94.884 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 95 CCD RIGAKU JUPITER 210 2004-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0000 SPring-8 BL45XU
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 2.3 20 96 0.093 18 7.2 23766 12.6
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) 1 2.3 2.38 93.1 0.213 8.5 7.2
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 2YQC 2.3 19.91 24196 1216 99.6 0.183 0.183 0.183 0.223 0.2248 RANDOM 21.4
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] -3.67 -2.47 6.13
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.29 c_scbond_it 2.42 c_mcangle_it 2.19 c_mcbond_it 1.45 c_angle_deg 1.3 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.29 c_scbond_it 2.42 c_mcangle_it 2.19 c_mcbond_it 1.45 c_angle_deg 1.3 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3653 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 57
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing