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Dihydrodipicolinate synthase (E. coli)- mutant R138A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 284 protein solution (~5 mg/ml in Tris.HCl 20 mM, pH 8, 2.5 uL), precipitant (K2HPO4 1.8 M, pH 10, 1.2 uL), and N-octyl- -R-glucopyranoside (6% w/v, 0.6 uL), VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties Matthews coefficient Solvent content 3.77 67.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.989 α = 90 b = 120.989 β = 90 c = 111.302 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 110 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.8 39.6 100 0.063 5.63 87227 87227
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) 1.8 1.86 100 0.394 4 5.43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.94 33.33 66352 66352 3515 100 0.16421 0.16281 0.1742 0.19142 0.2046 RANDOM 20.637
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] -0.24 -0.12 -0.24 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.142 r_dihedral_angle_4_deg 15.901 r_dihedral_angle_3_deg 13.557 r_dihedral_angle_1_deg 6.188 r_scangle_it 3.483 r_scbond_it 2.152 r_angle_refined_deg 1.339 r_mcangle_it 1.209 r_angle_other_deg 0.852 r_mcbond_it 0.632
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.142 r_dihedral_angle_4_deg 15.901 r_dihedral_angle_3_deg 13.557 r_dihedral_angle_1_deg 6.188 r_scangle_it 3.483 r_scbond_it 2.152 r_angle_refined_deg 1.339 r_mcangle_it 1.209 r_angle_other_deg 0.852 r_mcbond_it 0.632 r_symmetry_vdw_other 0.274 r_nbd_refined 0.23 r_nbd_other 0.181 r_symmetry_vdw_refined 0.17 r_nbtor_refined 0.165 r_mcbond_other 0.15 r_xyhbond_nbd_refined 0.137 r_metal_ion_refined 0.13 r_nbtor_other 0.087 r_symmetry_hbond_refined 0.086 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4301 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement AMoRE phasing