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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 8.5 277 20% w/v PEG 600, 0.15M KSCN, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.51 64.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.864 α = 90 b = 148.864 β = 90 c = 102.878 γ = 90
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 2003-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8125 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 3.151 20 99.8 0.195 7.7 5.3 19526 19526 70
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 3.151 3.2 99 0.79 1.7 4.4 971
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 3.151 19.55 19427 19028 399 100 0.23096 0.23096 0.22988 0.2304 0.27948 0.2746 RANDOM 52.835
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] 0.06 0.06 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.931 r_dihedral_angle_3_deg 21.639 r_dihedral_angle_4_deg 21.443 r_dihedral_angle_1_deg 6.877 r_scangle_it 1.969 r_angle_refined_deg 1.514 r_scbond_it 1.106 r_mcangle_it 1.037 r_mcbond_it 0.572 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.931 r_dihedral_angle_3_deg 21.639 r_dihedral_angle_4_deg 21.443 r_dihedral_angle_1_deg 6.877 r_scangle_it 1.969 r_angle_refined_deg 1.514 r_scbond_it 1.106 r_mcangle_it 1.037 r_mcbond_it 0.572 r_nbtor_refined 0.32 r_nbd_refined 0.258 r_symmetry_vdw_refined 0.245 r_symmetry_hbond_refined 0.194 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5201 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 34
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling