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Crystal structure of the omega transaminase from Pseudomonas jessenii in the apo form, crystallized from succinate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GRX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 1.0 M Sodium succinate, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.24 α = 90 b = 98.24 β = 90 c = 119.05 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH 2015-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 50.9 99.8 0.038 17 7.4 104659 16.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 95.3 0.402 2 5.8
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 4GRX 1.8 50.9 99354 5253 99.73 0.1418 0.14055 0.1533 0.16575 0.1757 RANDOM 24.737
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] -0.23 -0.23 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.482 r_dihedral_angle_4_deg 16.353 r_dihedral_angle_3_deg 11.871 r_long_range_B_refined 6.286 r_dihedral_angle_1_deg 6.118 r_long_range_B_other 5.993 r_scangle_other 2.215 r_scbond_it 1.373 r_scbond_other 1.373 r_angle_refined_deg 1.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.482 r_dihedral_angle_4_deg 16.353 r_dihedral_angle_3_deg 11.871 r_long_range_B_refined 6.286 r_dihedral_angle_1_deg 6.118 r_long_range_B_other 5.993 r_scangle_other 2.215 r_scbond_it 1.373 r_scbond_other 1.373 r_angle_refined_deg 1.345 r_mcangle_other 1.132 r_mcangle_it 1.131 r_angle_other_deg 0.985 r_mcbond_it 0.727 r_mcbond_other 0.726 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6936 Nucleic Acid Atoms Solvent Atoms 914 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing