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Crystal structure of the omega transaminase from Pseudomonas jessenii in the apo form, crystallized from ammonium phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G4B D_1200009303
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 1.0 M ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 2.9 0.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.296 α = 90 b = 98.296 β = 90 c = 119.924 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 2015-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 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 1.87 51.2 99.7 0.034 19.9 4.1 94352 18.6
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 1.87 1.9 94.9 0.357 2.1 3.4
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 FOURIER SYNTHESIS THROUGHOUT D_1200009303 1.87 51.2 89551 4739 99.72 0.1691 0.16789 0.1594 0.19207 0.1792 RANDOM 23.151
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] -0.2 -0.2 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.795 r_dihedral_angle_4_deg 15.717 r_dihedral_angle_3_deg 11.827 r_dihedral_angle_1_deg 6.148 r_long_range_B_refined 5.713 r_long_range_B_other 5.25 r_scangle_other 2.253 r_scbond_it 1.409 r_scbond_other 1.404 r_angle_refined_deg 1.398
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.795 r_dihedral_angle_4_deg 15.717 r_dihedral_angle_3_deg 11.827 r_dihedral_angle_1_deg 6.148 r_long_range_B_refined 5.713 r_long_range_B_other 5.25 r_scangle_other 2.253 r_scbond_it 1.409 r_scbond_other 1.404 r_angle_refined_deg 1.398 r_mcangle_other 1.3 r_mcangle_it 1.299 r_angle_other_deg 1.01 r_mcbond_it 0.831 r_mcbond_other 0.826 r_chiral_restr 0.083 r_bond_refined_d 0.01 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 6943 Nucleic Acid Atoms Solvent Atoms 832 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing