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Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans, in the substrate-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 5.7 293 30% PEG 6000, 0.1M ammonium sulfate, 5% glycerol, 0.01M N-acetylglucosamine-1-phosphate, 0.1M citrate, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.431 α = 90.01 b = 61.804 β = 97.72 c = 90.438 γ = 92.88
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 2004-12-06 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 50 93 0.07 11.2 2 43334 16.6
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 86.2 0.12 6.8 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 38.31 44027 2188 97.7 0.193 0.193 0.1925 0.238 0.2378 RANDOM 22.9
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] 2.13 1.29 1.24 0.63 -0.63 -2.76
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 894.2 c_scangle_it 3.1 c_scbond_it 2.15 c_mcangle_it 2.1 c_angle_deg 1.4 c_mcbond_it 1.35 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 894.2 c_scangle_it 3.1 c_scbond_it 2.15 c_mcangle_it 2.1 c_angle_deg 1.4 c_mcbond_it 1.35 c_bond_d 0.009 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_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 7259 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 55
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing