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Crystal structure of aminotransferase-like protein from Variovorax paradoxus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.1 293 0.1 M Citric acid bistris propane pH 4.1, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.64 66.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.299 α = 90 b = 164.299 β = 90 c = 190.419 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 2022-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
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 2.3 190.42 99.7 0.328 0.336 0.073 0.996 7.5 20.5 131283
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 2.3 2.34 99.5 3.019 3.091 0.659 0.635 21.3
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 (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 5CM0 2.3 142.29 124626 6635 99.64 0.2066 0.2054 0.2069 0.2275 0.2285 RANDOM 42.883
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] -0.09 -0.04 -0.09 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.145 r_dihedral_angle_4_deg 20.516 r_dihedral_angle_3_deg 16.369 r_dihedral_angle_1_deg 7.514 r_angle_refined_deg 2.216 r_chiral_restr 0.15 r_bond_refined_d 0.016 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13495 Nucleic Acid Atoms Solvent Atoms 611 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction DIALS data reduction REFMAC phasing