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6-phosphogluconolactonase from Trypanosoma cruzi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EB9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.3 298 0.1 M sodium citrate,
3.5 mM DTT,
cryo-soak in 30% glycerol
Crystal Properties Matthews coefficient Solvent content 3.03 59.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.77 α = 90 b = 63.39 β = 94.91 c = 79.32 γ = 90
Symmetry Space Group P 1 2 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 ADSC QUANTUM 210 2005-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.9796 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.95 50.9 95.8 0.245 0.288 0.15 0.971 4.9 3.6 49639
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 77.7 1.669 2.014 1.106 0.472 3.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3eb9 1.95 49.497 49552 2543 95.329 0.233 0.2312 0.2438 0.2699 0.2809 24.828
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] 1.496 -0.389 -2.648 1.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.677 r_dihedral_angle_3_deg 16.495 r_dihedral_angle_4_deg 10.893 r_dihedral_angle_1_deg 7.337 r_lrange_it 6.49 r_lrange_other 6.49 r_scangle_it 4.221 r_scangle_other 4.22 r_mcangle_it 3.509 r_mcangle_other 3.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.677 r_dihedral_angle_3_deg 16.495 r_dihedral_angle_4_deg 10.893 r_dihedral_angle_1_deg 7.337 r_lrange_it 6.49 r_lrange_other 6.49 r_scangle_it 4.221 r_scangle_other 4.22 r_mcangle_it 3.509 r_mcangle_other 3.508 r_scbond_it 2.688 r_scbond_other 2.688 r_mcbond_it 2.185 r_mcbond_other 2.184 r_angle_refined_deg 1.626 r_angle_other_deg 1.287 r_nbd_other 0.215 r_nbd_refined 0.213 r_symmetry_xyhbond_nbd_refined 0.203 r_xyhbond_nbd_refined 0.197 r_symmetry_nbd_refined 0.186 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.151 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.075 r_xyhbond_nbd_other 0.073 r_ncsr_local_group_1 0.066 r_symmetry_xyhbond_nbd_other 0.016 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4059 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 33
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MoRDa phasing