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High-resolution structure of chorismate mutase from Corynebacterium glutamicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VKL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 293 100 mM NH4 formate, pH 6.6
100 mM KSCN
30% PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 1.93 36.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.858 α = 90 b = 24.627 β = 99.43 c = 38.546 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M 2014-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97908 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 1.06 40.87 87.9 0.056 8.96 4.3 30562
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 1.06 1.13 49.2 1.937 0.44 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 2VKL 1.06 40.87 29317 1558 87.65 0.17548 0.17325 0.182 0.22021 0.2223 RANDOM 20.591
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] 1.5 -0.63 -0.92 -0.35
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.189 r_dihedral_angle_2_deg 24.84 r_dihedral_angle_4_deg 20.121 r_sphericity_bonded 15.208 r_dihedral_angle_3_deg 15.086 r_dihedral_angle_1_deg 4.697 r_long_range_B_refined 3.711 r_rigid_bond_restr 3.706 r_long_range_B_other 3.254 r_scangle_other 2.477
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.189 r_dihedral_angle_2_deg 24.84 r_dihedral_angle_4_deg 20.121 r_sphericity_bonded 15.208 r_dihedral_angle_3_deg 15.086 r_dihedral_angle_1_deg 4.697 r_long_range_B_refined 3.711 r_rigid_bond_restr 3.706 r_long_range_B_other 3.254 r_scangle_other 2.477 r_mcangle_other 2.258 r_mcangle_it 2.208 r_scbond_it 2.135 r_angle_refined_deg 2.012 r_scbond_other 2.007 r_mcbond_other 1.789 r_mcbond_it 1.763 r_angle_other_deg 1.282 r_chiral_restr 0.115 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 629 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PHASER phasing Aimless data scaling XDS data reduction XDS data scaling