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Crystal structure of 4-Amino-4-deoxychorismate lyase from Micromonospora aurantiaca ATCC 27029 (holo form) in complex with chorismate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 288 100 mM HEPES buffer, pH 7.0, 10 mM MgCl2, 5 mM NiCl2, 20% (v/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.741 α = 90 b = 88.9 β = 90 c = 70.333 γ = 90
Symmetry Space Group C 2 2 21
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 RIGAKU HyPix-6000HE 2026-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54184
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 1.85 21.89 99.4 0.182 0.191 0.059 0.995 12.7 10.2 22873
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 1.85 1.89 96.4 0.799 0.857 0.299 0.759 7.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.85 21.89 21723 1136 99.22 0.16697 0.16477 0.1764 0.21037 0.2227 RANDOM 12.892
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] -0.4 -0.18 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.324 r_dihedral_angle_4_deg 15.696 r_dihedral_angle_3_deg 14.337 r_dihedral_angle_1_deg 6.957 r_long_range_B_refined 4.092 r_long_range_B_other 3.803 r_scangle_other 2.581 r_angle_refined_deg 1.731 r_scbond_it 1.688 r_scbond_other 1.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.324 r_dihedral_angle_4_deg 15.696 r_dihedral_angle_3_deg 14.337 r_dihedral_angle_1_deg 6.957 r_long_range_B_refined 4.092 r_long_range_B_other 3.803 r_scangle_other 2.581 r_angle_refined_deg 1.731 r_scbond_it 1.688 r_scbond_other 1.688 r_mcangle_it 1.618 r_mcangle_other 1.617 r_angle_other_deg 1.391 r_mcbond_it 1.037 r_mcbond_other 1.036 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 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 2078 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction CrysalisPro data reduction MOLREP phasing