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Dihydrodipicolinate synthase S48F with pyruvate and succinic semi-aldehyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YXC PDB entry 1YXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294.15 glucopyranoside, potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 3.68 66.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.919 α = 90 b = 120.919 β = 90 c = 110.081 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 315r 2011-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95369 Australian Synchrotron MX2
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 33.34 100 0.086 17.5 11 83589
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.86 0.329 0.156
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 PDB entry 1YXC 1.82 33.27 78999 4156 99.96 0.14457 0.14318 0.1567 0.17075 0.1797 RANDOM 19.835
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 34.443 r_dihedral_angle_4_deg 18.446 r_dihedral_angle_3_deg 13.147 r_dihedral_angle_1_deg 6.328 r_long_range_B_other 5.947 r_long_range_B_refined 5.946 r_scangle_other 4.461 r_scbond_it 3.173 r_scbond_other 3.128 r_mcangle_other 2.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.443 r_dihedral_angle_4_deg 18.446 r_dihedral_angle_3_deg 13.147 r_dihedral_angle_1_deg 6.328 r_long_range_B_other 5.947 r_long_range_B_refined 5.946 r_scangle_other 4.461 r_scbond_it 3.173 r_scbond_other 3.128 r_mcangle_other 2.609 r_mcangle_it 2.603 r_angle_refined_deg 2.218 r_mcbond_it 2.059 r_mcbond_other 2.05 r_angle_other_deg 1.206 r_chiral_restr 0.152 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 4319 Nucleic Acid Atoms Solvent Atoms 649 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement Aimless data scaling Coot model building PHASER phasing