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DAHP synthase from Corynebacterium glutamicum in complex with tryptophan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 277 100 mM NH4 formate, pH 6.6, 100 mM KSCN, 30% PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 4.62 73.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.189 α = 90 b = 109.189 β = 90 c = 279.897 γ = 120
Symmetry Space Group P 62 2 2
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 2014-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
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 2.65 37.01 99.7 0.28 9.39 17.36 29830
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 2.65 2.8 98.8 7.276 0.39 17.85
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 2B7O 2.65 37.01 28128 1436 99.81 0.24857 0.24675 0.2512 0.28463 0.2823 RANDOM 108.112
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] 3.61 1.81 3.61 -11.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.518 r_dihedral_angle_3_deg 16.251 r_dihedral_angle_4_deg 13.4 r_long_range_B_other 9.192 r_long_range_B_refined 9.19 r_dihedral_angle_1_deg 6.122 r_mcangle_it 6.117 r_mcangle_other 6.116 r_scangle_other 5.73 r_mcbond_other 3.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.518 r_dihedral_angle_3_deg 16.251 r_dihedral_angle_4_deg 13.4 r_long_range_B_other 9.192 r_long_range_B_refined 9.19 r_dihedral_angle_1_deg 6.122 r_mcangle_it 6.117 r_mcangle_other 6.116 r_scangle_other 5.73 r_mcbond_other 3.784 r_mcbond_it 3.783 r_scbond_it 3.416 r_scbond_other 3.411 r_angle_refined_deg 1.257 r_angle_other_deg 0.921 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 3456 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement PHASER phasing XDS data reduction Aimless data scaling