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The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase with Gly190Pro mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NV8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 20 mM BTP, 150 mM NaCl, 0.5 mM TCEP, 0.2 mM PEP, 0.1 mM MnCl2, 2M Li2SO4, 2% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.94 68.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.251 α = 90 b = 204.251 β = 90 c = 66.551 γ = 120
Symmetry Space Group P 32 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 CCD ADSC QUANTUM 210r 2014-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95370 Australian Synchrotron MX1
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 1.9 51.06 99.9 0.131 0.136 0.035 0.995 16.9 14.3 124730
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 1.9 1.93 99.5 1.333 1.429 0.488 0.345 7.4
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 (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 3NV8 1.9 36.83 118485 6226 99.82 0.1588 0.1577 0.158 0.1799 0.1777 RANDOM 20.536
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] 2.05 2.05 -4.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.631 r_dihedral_angle_4_deg 18.071 r_dihedral_angle_3_deg 14.063 r_dihedral_angle_1_deg 6.312 r_angle_refined_deg 1.435 r_angle_other_deg 1.358 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.631 r_dihedral_angle_4_deg 18.071 r_dihedral_angle_3_deg 14.063 r_dihedral_angle_1_deg 6.312 r_angle_refined_deg 1.435 r_angle_other_deg 1.358 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6479 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing