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Dihydrodipicolinate synthase mutant S48F with lysine in the allosteric site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 249.15 glucopyrdoside, Dipotassium phosphate
Crystal Properties Matthews coefficient Solvent content 3.71 66.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.049 α = 90 b = 121.049 β = 90 c = 110.151 γ = 120
Symmetry Space Group P 31 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 294.15 CCD ADSC QUANTUM 210r 2011-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95369 Australian Synchrotron MX1
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 1.82 33.3 100 0.137 11.7 10.8 83378
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.86 0.846
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 1yxc 1.82 33.31 79187 4161 99.97 0.14468 0.14332 0.1566 0.16984 0.18 RANDOM 18.309
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.138 r_dihedral_angle_4_deg 16.918 r_dihedral_angle_3_deg 13.054 r_dihedral_angle_1_deg 6.162 r_long_range_B_other 5.787 r_long_range_B_refined 5.786 r_scangle_other 4.449 r_scbond_it 3.066 r_scbond_other 3.065 r_mcangle_other 2.442
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.138 r_dihedral_angle_4_deg 16.918 r_dihedral_angle_3_deg 13.054 r_dihedral_angle_1_deg 6.162 r_long_range_B_other 5.787 r_long_range_B_refined 5.786 r_scangle_other 4.449 r_scbond_it 3.066 r_scbond_other 3.065 r_mcangle_other 2.442 r_mcangle_it 2.441 r_angle_refined_deg 2.168 r_mcbond_it 1.88 r_mcbond_other 1.877 r_angle_other_deg 1.176 r_chiral_restr 0.153 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4313 Nucleic Acid Atoms Solvent Atoms 650 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling PHASER phasing