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Ornithine aminotransferase PY00104 from Plasmodium Yoelii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 298 VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.489 α = 90 b = 221.829 β = 100.89 c = 114.484 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 CCD ADSC QUANTUM 210 2005-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 50 99.8 0.051 24.5 3.9 158741 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.18 100 0.43 2.7 3.8
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 2OAT 2.1 49.74 150728 7970 99.13 0.21703 0.21483 0.2144 0.25885 0.2582 RANDOM 41.45
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] 0.5 1.03 0.77 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.27 r_dihedral_angle_3_deg 17.922 r_dihedral_angle_4_deg 14.958 r_dihedral_angle_1_deg 5.884 r_scangle_it 4.627 r_scbond_it 3.206 r_mcangle_it 2.498 r_mcbond_it 1.604 r_angle_refined_deg 1.378 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.27 r_dihedral_angle_3_deg 17.922 r_dihedral_angle_4_deg 14.958 r_dihedral_angle_1_deg 5.884 r_scangle_it 4.627 r_scbond_it 3.206 r_mcangle_it 2.498 r_mcbond_it 1.604 r_angle_refined_deg 1.378 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17647 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing