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Crystal Structure of Dihydrodipicolinate synthase (DHDPS) from Brucella suis 1330
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I7U PDB entry 4i7u as per MORDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 287 Qiagen JCSG Core-1 screen, f12: 40% (V/V) MPD, 100mM sodium phosphate dibasic / citric acid pH 4.2: BrsuA.01563.a.A1.PW34594; tray 231309f12, cryo, 20%EG, puck atd2-7
Crystal Properties Matthews coefficient Solvent content 2.29 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.65 α = 90 b = 86.65 β = 90 c = 142.97 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r Si(220) 2012-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.2 43.33 99.1 0.125 0.141 0.993 11.74 4.633 60445 28.674
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 98.2 0.566 0.639 0.804 2.64 4.626
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 4i7u as per MORDA 2.2 43.33 58503 1935 99.14 0.1357 0.1348 0.1596 0.162 0.1773 RANDOM 20.617
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] -21.39 -21.39 42.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.24 r_dihedral_angle_4_deg 16.131 r_dihedral_angle_3_deg 13.85 r_dihedral_angle_1_deg 6.723 r_angle_refined_deg 1.625 r_angle_other_deg 1.346 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.24 r_dihedral_angle_4_deg 16.131 r_dihedral_angle_3_deg 13.85 r_dihedral_angle_1_deg 6.723 r_angle_refined_deg 1.625 r_angle_other_deg 1.346 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8786 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 77
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MoRDa phasing Coot model building