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Crystal structure of human R180T variant of ORNITHINE AMINOTRANSFERASE at 1.8 Angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 Prot 115uM in 150mM NaCl 50mM Hepes pH 8.0 mixed with hit 1-5 of the LMB screen (Molecular Dimensions): 4 M Ammonium acetate 0.1 M Bis-Tris propane 7.0 (cryo + Glycerol 20%)
Crystal Properties Matthews coefficient Solvent content 2.12 41.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.252 α = 90 b = 193.252 β = 90 c = 57.211 γ = 120
Symmetry Space Group P 31 1 2
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 2M 2017-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.999995 ELETTRA 5.2R
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 1.8 48.31 98.7 0.136 0.145 0.049 0.997 7.6 8 110536
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 1.8 1.83 96.2 0.398 0.444 0.192 0.94 5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1OAT 1.8 45 105147 5358 98.56 0.2212 0.2209 0.2277 0.2199 RANDOM 15.819
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] -0.37 -0.19 -0.37 1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_dihedral_angle_4_deg 17.18 r_dihedral_angle_3_deg 13.391 r_dihedral_angle_1_deg 5.79 r_angle_other_deg 3.57 r_angle_refined_deg 1.473 r_chiral_restr 0.067 r_gen_planes_other 0.024 r_bond_refined_d 0.021 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_dihedral_angle_4_deg 17.18 r_dihedral_angle_3_deg 13.391 r_dihedral_angle_1_deg 5.79 r_angle_other_deg 3.57 r_angle_refined_deg 1.473 r_chiral_restr 0.067 r_gen_planes_other 0.024 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9139 Nucleic Acid Atoms Solvent Atoms 1200 Heterogen Atoms 45
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction