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Crystal structure of the omega TRANSAMINASE FROM PSEUDOMONAS Jessenii in complex with PMP
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 Sodium succinate pH 7.5, 0.1 mM PLP
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.562 α = 90 b = 97.562 β = 90 c = 119.372 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 2015-11-19 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 2.5 50.9 100 0.062 12 4.2 38677 30.2
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 2.5 2.6 99.9 0.42 2.1 4.2
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 2.5 50.9 36655 1978 99.9 0.16216 0.15999 0.167 0.20326 0.2042 RANDOM 38.361
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] 0.48 0.48 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.59 r_dihedral_angle_4_deg 14.383 r_dihedral_angle_3_deg 13.68 r_dihedral_angle_1_deg 5.983 r_long_range_B_refined 5.331 r_long_range_B_other 5.33 r_scangle_other 3.972 r_mcangle_it 3.097 r_mcangle_other 3.097 r_scbond_it 2.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.59 r_dihedral_angle_4_deg 14.383 r_dihedral_angle_3_deg 13.68 r_dihedral_angle_1_deg 5.983 r_long_range_B_refined 5.331 r_long_range_B_other 5.33 r_scangle_other 3.972 r_mcangle_it 3.097 r_mcangle_other 3.097 r_scbond_it 2.376 r_scbond_other 2.376 r_mcbond_it 1.96 r_mcbond_other 1.958 r_angle_refined_deg 1.308 r_angle_other_deg 0.886 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 288 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing