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Crystal structure of guanidinase from Nitrospira inopinata
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 295.15 0.5 M (NH4)2SO4, 0.1 M Na3 Citrate pH 5.6, 1 M Li2SO4 2 VAPOR DIFFUSION, SITTING DROP 5.6 295.15 0.5 M (NH4)2SO4, 0.1 M Na3 Citrate pH 5.6, 1 M Li2SO4 3 VAPOR DIFFUSION, SITTING DROP 5.6 295.15 0.5 M (NH4)2SO4, 0.1 M Na3 Citrate pH 5.6, 1 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.35 47.55 2.35 47.55 2.35 47.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.965 α = 90 b = 164.791 β = 90.03 c = 143.965 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 PIXEL DECTRIS PILATUS 6M Vertical CRL / Horizontal Eliptical mirror 2022-06-04 M SINGLE WAVELENGTH 2 2 x-ray 100 PIXEL DECTRIS PILATUS 6M Vertical CRL / Horizontal Eliptical mirror 2023-12-05 M SINGLE WAVELENGTH 3 3 x-ray 100 PIXEL DECTRIS PILATUS 6M Vertical CRL / Horizontal Eliptical mirror 2023-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9184 ESRF ID30B 2 SYNCHROTRON ESRF BEAMLINE ID30B 1.48253 ESRF ID30B 3 SYNCHROTRON ESRF BEAMLINE ID30B 1.89289 ESRF ID30B
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 1.58 45.01 92.89 0.1064 0.1318 0.07673 0.991 4.66 2.3 583936 22.07
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 1.58 1.636 85.24 1.191 1.506 0.9081 0.256 0.56 2.1
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 1.58 45.01 1.33 583176 2001 92.9 0.1999 0.1998 0.1999 0.2142 0.214
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 14.52 f_angle_d 1.092 f_chiral_restr 0.065 f_plane_restr 0.013 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 34269 Nucleic Acid Atoms Solvent Atoms 2815 Heterogen Atoms 144
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PHASER phasing