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GABA-transaminase A1R958 in complex with external aldimine PLP-GABA adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ATP PDB ENTRY 4ATP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 28% (W/V) PEG3350, 0.2M AMMONIUM ACETATE, 1MM PLP, 3% (V/V) DIOXANE, 10 MM GABA, 100 MM BIS-TRIS PROPANE PH 7.5, PROTEIN AT 10 MG PER ML.
Crystal Properties Matthews coefficient Solvent content 2.42 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.71 α = 90 b = 292.83 β = 90 c = 105.96 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC CCD 2012-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.75 97.61 100 0.12 14.3 7.4 136067 2
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) 1 2.75 2.82 100 0.74 2.6 7.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4ATP 2.75 90.87 136067 7182 99.97 0.20407 0.20177 0.2011 0.24803 0.2435 RANDOM 35.05
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] -0.63 -0.95 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.711 r_dihedral_angle_3_deg 14.863 r_dihedral_angle_4_deg 14.533 r_dihedral_angle_1_deg 5.608 r_angle_refined_deg 1.451 r_angle_other_deg 1.385 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_bond_other_d 0.008 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.711 r_dihedral_angle_3_deg 14.863 r_dihedral_angle_4_deg 14.533 r_dihedral_angle_1_deg 5.608 r_angle_refined_deg 1.451 r_angle_other_deg 1.385 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37887 Nucleic Acid Atoms Solvent Atoms 546 Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement xia2 data scaling MOLREP phasing