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Crystal Structure Analysis of a mutant of DIHYDRODIPICOLINATE SYNTHASE--residue Tyr133 to Phe133
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 Drop contains: 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 66.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.206 α = 90 b = 121.206 β = 90 c = 110.784 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 2002-11-20 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 2.32 50 99.7 0.094 40716
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) 2.32 2.38 99.6 0.318
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 2.32 20.16 38651 2038 100 0.17968 0.17968 0.17807 0.185 0.21093 0.2139 RANDOM 27.065
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_1_deg 6.211 r_scangle_it 2.678 r_scbond_it 1.504 r_angle_refined_deg 1.318 r_mcangle_it 0.914 r_angle_other_deg 0.857 r_mcbond_it 0.467 r_nbd_other 0.235 r_symmetry_vdw_refined 0.219 r_symmetry_vdw_other 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.211 r_scangle_it 2.678 r_scbond_it 1.504 r_angle_refined_deg 1.318 r_mcangle_it 0.914 r_angle_other_deg 0.857 r_mcbond_it 0.467 r_nbd_other 0.235 r_symmetry_vdw_refined 0.219 r_symmetry_vdw_other 0.209 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.128 r_nbtor_other 0.124 r_chiral_restr 0.076 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 4321 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling