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Dihydrodipicolinate synthase (E. coli)- mutant R138H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 10 285 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, temperature 12K
Crystal Properties Matthews coefficient Solvent content 3.76 67.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.016 α = 90 b = 121.016 β = 90 c = 111.414 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 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) 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 2.05 33.3 99.7 59240
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) 2.05 33.3 99.7 0.087 10.4 4.2 59240
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.05 32.27 56283 2951 100 0.184 0.18252 0.1921 0.2128 0.224 RANDOM 23.345
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] -0.25 -0.12 -0.25 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.763 r_dihedral_angle_4_deg 14.627 r_dihedral_angle_3_deg 14.349 r_dihedral_angle_1_deg 5.893 r_scangle_it 1.87 r_scbond_it 1.11 r_angle_refined_deg 1.106 r_angle_other_deg 0.799 r_mcangle_it 0.685 r_mcbond_it 0.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.763 r_dihedral_angle_4_deg 14.627 r_dihedral_angle_3_deg 14.349 r_dihedral_angle_1_deg 5.893 r_scangle_it 1.87 r_scbond_it 1.11 r_angle_refined_deg 1.106 r_angle_other_deg 0.799 r_mcangle_it 0.685 r_mcbond_it 0.356 r_symmetry_vdw_other 0.219 r_nbd_refined 0.213 r_nbd_other 0.173 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.12 r_symmetry_hbond_refined 0.111 r_symmetry_vdw_refined 0.09 r_nbtor_other 0.086 r_metal_ion_refined 0.082 r_chiral_restr 0.065 r_mcbond_other 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 4323 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement AMoRE phasing