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GTP Cyclohydrolase-IB with sodium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K95
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES Na, 1.6 M ammonium sulfate, 2% PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.03 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.499 α = 90 b = 116.499 β = 90 c = 70.806 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS EIGER X 16M 2022-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 2.03 41.08 99.93 0.2366 0.2429 0.0546 0.998 13.5 19.8 36073 38.16
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 2.03 2.103 99.77 1.719 1.771 0.4239 0.826 1.67 17
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 2.03 41.08 1.35 36064 1810 99.96 0.2012 0.1993 0.1998 0.2277 0.228 42.62
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 12.619 f_angle_d 1.6694 f_chiral_restr 0.0946 f_bond_d 0.0128 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3911 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing