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Crystal Structure Analysis of a mutant of DIHYDRODIPICOLINATE SYNTHASE--residue Tyr107 to Phe107
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 277 potassium phosphate (0.0012ml, 1.8M, pH10), N-octyl-beta-R-glucopyrandoside (0.0006ml, 6% w/v), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.65 66.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.888 α = 90 b = 120.888 β = 90 c = 110.202 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 MARRESEARCH 2002-10-20 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 2.35 50 98.6 0.114 38813
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 2.35 2.41 95.4 0.28
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 (All) 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 1DHP 2.35 20.94 36809 1942 100 0.19705 0.19705 0.19523 0.199 0.23174 0.232 RANDOM 27.689
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] -1.3 -0.65 -1.3 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.998 r_scangle_it 2.363 r_scbond_it 1.323 r_angle_refined_deg 1.313 r_mcangle_it 0.882 r_angle_other_deg 0.871 r_mcbond_it 0.464 r_nbd_other 0.235 r_symmetry_vdw_other 0.199 r_nbd_refined 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.998 r_scangle_it 2.363 r_scbond_it 1.323 r_angle_refined_deg 1.313 r_mcangle_it 0.882 r_angle_other_deg 0.871 r_mcbond_it 0.464 r_nbd_other 0.235 r_symmetry_vdw_other 0.199 r_nbd_refined 0.198 r_nbtor_other 0.152 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.091 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4317 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling