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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 2-amino-2-deoxy-D-mannitol 6-phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.121 α = 90 b = 118.167 β = 91.87 c = 100.137 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 2006-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8162 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 99.6 0.058 22 4.1 120934 120934 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 94.7 0.474 2.3 3.8 5743
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 19.93 120507 118083 2424 100 0.17203 0.17203 0.17121 0.1716 0.21164 0.2122 RANDOM 25.539
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 32.678 r_dihedral_angle_4_deg 19.009 r_dihedral_angle_3_deg 14.65 r_dihedral_angle_1_deg 5.831 r_scangle_it 4.533 r_scbond_it 2.882 r_mcangle_it 1.812 r_angle_refined_deg 1.675 r_mcbond_it 1.033 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.678 r_dihedral_angle_4_deg 19.009 r_dihedral_angle_3_deg 14.65 r_dihedral_angle_1_deg 5.831 r_scangle_it 4.533 r_scbond_it 2.882 r_mcangle_it 1.812 r_angle_refined_deg 1.675 r_mcbond_it 1.033 r_nbtor_refined 0.307 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.148 r_symmetry_vdw_refined 0.139 r_chiral_restr 0.12 r_metal_ion_refined 0.101 r_symmetry_metal_ion_refined 0.047 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10658 Nucleic Acid Atoms Solvent Atoms 769 Heterogen Atoms 232
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling