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Crystal structure of cytosolic HPPK-DHPS from A.thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BMB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Crystals of 13-20 mg/ml HPPK-DHPS (purified in 20 mM HEPES pH 8.0, 125 mM sodium chloride, 2 mM dithiothreitol of buffer) were obtained in 30-40% PEG 3350 and 0.2M NaF
Crystal Properties Matthews coefficient Solvent content 2.65 53.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.68 α = 90 b = 240.15 β = 90 c = 148.88 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.3 93.46 96.9 0.09 0.1 0.04 0.99 9.6 5.9 51863 51.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.37 77.7 0.639 0.746 0.377 0.23 3.6
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2BMB 2.3 93.46 51836 3249 96.734 0.242 0.238 0.2525 0.2998 0.3092 67.247
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] 6.057 -5.568 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.989 r_dihedral_angle_4_deg 20.688 r_dihedral_angle_3_deg 18.782 r_dihedral_angle_1_deg 6.355 r_angle_refined_deg 1.6 r_angle_other_deg 1.223 r_nbd_other 0.231 r_nbd_refined 0.205 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.989 r_dihedral_angle_4_deg 20.688 r_dihedral_angle_3_deg 18.782 r_dihedral_angle_1_deg 6.355 r_angle_refined_deg 1.6 r_angle_other_deg 1.223 r_nbd_other 0.231 r_nbd_refined 0.205 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.16 r_symmetry_nbd_refined 0.16 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6679 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing PHENIX model building