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Crystal structure of 6-dimethylallyltryptophan synthase from Micromonospora olivasterospora in complex with DMASPP and Trp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5INJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 200 mM Calcium acetate, 26% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.021 α = 90 b = 98.471 β = 107.487 c = 89.185 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 16M 2017-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00001 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.69 39.673 98.5 0.09 0.99 11.3 4 143483 30.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.79 98.5 0.68 0.82 2.1 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5INJ 1.7 39.673 139303 1671 98.729 0.202 0.2021 0.2109 0.2302 0.2351 23.708
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] 0.944 -0.324 0.041 -0.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.02 r_dihedral_angle_4_deg 16.905 r_dihedral_angle_3_deg 12.828 r_dihedral_angle_1_deg 5.971 r_lrange_it 4.173 r_lrange_other 4.156 r_mcangle_it 2.011 r_mcangle_other 2.011 r_scangle_it 1.982 r_scangle_other 1.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.02 r_dihedral_angle_4_deg 16.905 r_dihedral_angle_3_deg 12.828 r_dihedral_angle_1_deg 5.971 r_lrange_it 4.173 r_lrange_other 4.156 r_mcangle_it 2.011 r_mcangle_other 2.011 r_scangle_it 1.982 r_scangle_other 1.982 r_angle_refined_deg 1.246 r_angle_other_deg 1.213 r_scbond_it 1.203 r_scbond_other 1.202 r_mcbond_it 1.174 r_mcbond_other 1.174 r_nbd_refined 0.185 r_nbd_other 0.176 r_symmetry_nbd_refined 0.172 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.151 r_xyhbond_nbd_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.131 r_symmetry_xyhbond_nbd_other 0.085 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.053 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10771 Nucleic Acid Atoms Solvent Atoms 971 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement PHASER phasing XSCALE data scaling XDS data reduction