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The crystal structure of isomerase domain of glucosamine-6-phosphate synthase from Candida albicans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2POC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, 30% v/v 2-methyl-2,4-pentanediol, 10-fold excess of UDP-GlcNAc and Glc-6-P; crystals soaked with large excess of Fru-6-P, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.4 48.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.028 α = 90 b = 118.188 β = 91.78 c = 100.032 γ = 90
Symmetry Space Group P 1 21 1
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 MAR CCD 165 mm 2006-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.81620 EMBL/DESY, HAMBURG X11
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 1.9 20 99.7 0.08 22 7 120651 120651 23.2
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 1.9 1.93 98.4 0.569 3 6.1 5965
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2POC 1.9 19.94 120111 117692 2419 100 0.17165 0.17165 0.17074 0.171 0.21508 0.2153 RANDOM 25.584
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.026 r_dihedral_angle_4_deg 17.896 r_dihedral_angle_3_deg 14.524 r_dihedral_angle_1_deg 6.607 r_scangle_it 4.618 r_scbond_it 2.892 r_mcangle_it 1.86 r_angle_refined_deg 1.687 r_mcbond_it 1.054 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.026 r_dihedral_angle_4_deg 17.896 r_dihedral_angle_3_deg 14.524 r_dihedral_angle_1_deg 6.607 r_scangle_it 4.618 r_scbond_it 2.892 r_mcangle_it 1.86 r_angle_refined_deg 1.687 r_mcbond_it 1.054 r_nbtor_refined 0.307 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.196 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.115 r_metal_ion_refined 0.11 r_symmetry_metal_ion_refined 0.035 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10705 Nucleic Acid Atoms Solvent Atoms 748 Heterogen Atoms 232
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling