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Crystal structure of the omega transaminase from Chromobacterium violaceum in complex with PMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 Drops of 200 nl protein at 7.5 mg/ml mixed with 200 nl of 100 mM HEPES pH 7.5, 350 mM NaCl, 22.5 % w/v PEG 4000, 0.1 mM PLP
Crystal Properties Matthews coefficient Solvent content 2 38.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.909 α = 75.07 b = 61.973 β = 81.31 c = 118.81 γ = 75.3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2016-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.984 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.67 48.04 91.9 0.091 0.111 0.061 0.993 5.3 2.4 172591
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 87 0.646 0.81 0.48 0.654 2.3
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 4A6T 1.67 48.09 163935 8608 91.94 0.1618 0.1606 0.1728 0.1847 0.1945 RANDOM 25.689
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] 0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.889 r_dihedral_angle_4_deg 17.881 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_1_deg 7.068 r_angle_refined_deg 1.756 r_angle_other_deg 1.538 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.889 r_dihedral_angle_4_deg 17.881 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_1_deg 7.068 r_angle_refined_deg 1.756 r_angle_other_deg 1.538 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14255 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction