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DIHYDRONEOPTERIN ALDOLASE (DHNA) FROM YERSINIA PESTIS with alkylated Cys50 CO-CRYSTALLIZED with 7,8-dihydroneopterin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OJO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.05 - 0.1M BisTris, 0.1-0.2 M CaCl2, 0 - 0.1M NaCl, 43 - 49% MPD
Crystal Properties Matthews coefficient Solvent content 2.16 43.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.604 α = 90 b = 72.604 β = 90 c = 105.96 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 PIXEL DECTRIS PILATUS 200K 2021-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.65 50 91.8 0.043 0.05 0.025 9.7 3.5 7332
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 2.65 2.7 90.7 0.206 0.252 0.141 0.943 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6ojo 2.65 36.87 1.34 7323 722 91.65 0.2109 0.2054 0.2133 0.2579 0.2603 53.2409
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 f_dihedral_angle_d 17.332 f_angle_d 0.942 f_chiral_restr 0.061 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1810 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 70
Software Software Software Name Purpose HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing