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Structure of the old yellow enzyme from Trypanosoma cruzi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E2B PDB ENTRY 4E2B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 28% (w/v) polyethylene glycol 1500, 0.3 M ammonium fluoride and 10% DMSO, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.96 37.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.774 α = 90 b = 118.469 β = 90.09 c = 111.123 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 MARMOSAIC 225 mm CCD 2012-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.46 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.997 40 90.9 0.069 3.9 155841 80586 1 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.997 2.07 99.9 0.251 4
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 PDB ENTRY 4E2B 1.997 40 80586 76225 4013 90.08 0.2014 0.19599 0.19358 0.2085 0.24207 0.2608 RANDOM 24.694
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] 0.2 -0.84 -0.86 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.279 r_dihedral_angle_4_deg 19.25 r_dihedral_angle_3_deg 15.378 r_dihedral_angle_1_deg 6.609 r_angle_refined_deg 1.645 r_chiral_restr 0.112 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11832 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 140
Software Software Software Name Purpose NatXray data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling