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DAHP synthase from Corynebacterium glutamicum
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 8.7 277 100 mM Tris/bicine buffer
13% MPD
13% PEG 1000
13% PEG 3350
2% triethylene glycol
200 uM PEP
100 uM MnCl2
Crystal Properties Matthews coefficient Solvent content 4.66 73.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.844 α = 90 b = 109.844 β = 90 c = 279.304 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 2014-05-17 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 2.45 95.13 98.9 0.099 14.02 12.86 36845
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 2.45 2.6 87.4 2.95 0.64 10.46
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 2.45 20 34813 1884 97.62 0.24353 0.24303 0.247 0.25244 0.2568 RANDOM 111.803
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] 3.85 1.92 3.85 -12.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.245 r_dihedral_angle_3_deg 16.276 r_dihedral_angle_4_deg 11.068 r_long_range_B_refined 8.835 r_long_range_B_other 8.835 r_mcangle_it 5.976 r_mcangle_other 5.976 r_dihedral_angle_1_deg 5.822 r_scangle_other 5.285 r_mcbond_it 3.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.245 r_dihedral_angle_3_deg 16.276 r_dihedral_angle_4_deg 11.068 r_long_range_B_refined 8.835 r_long_range_B_other 8.835 r_mcangle_it 5.976 r_mcangle_other 5.976 r_dihedral_angle_1_deg 5.822 r_scangle_other 5.285 r_mcbond_it 3.651 r_mcbond_other 3.648 r_scbond_it 3.161 r_scbond_other 3.16 r_angle_refined_deg 1.177 r_angle_other_deg 0.907 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 3472 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement PHASES phasing Aimless data scaling XDS data scaling XDS data reduction