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Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with 5-phenylpyridin-2-ylmethylphosphonic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EGH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 0.1M sodium citrate, 0.8M sodium malonate, 0.3M potassium sodium (+) tartrate, 3mM NADPH, 5mM MgCl2, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.57 52.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.329 α = 90 b = 59.223 β = 90 c = 87.028 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210 2010-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 50 99.4 3.7 64644 64256 0.0001 0.0001
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 98.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2EGH 2 29.2 61352 60953 3253 99.35 0.19366 0.19246 0.21646 0.2068 RANDOM 23.593
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] 0.16 0.47 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.978 r_dihedral_angle_4_deg 21.205 r_dihedral_angle_3_deg 14.484 r_dihedral_angle_1_deg 5.083 r_scangle_it 4.922 r_scbond_it 3.208 r_mcangle_it 1.83 r_angle_refined_deg 1.621 r_mcbond_it 1.458 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.978 r_dihedral_angle_4_deg 21.205 r_dihedral_angle_3_deg 14.484 r_dihedral_angle_1_deg 5.083 r_scangle_it 4.922 r_scbond_it 3.208 r_mcangle_it 1.83 r_angle_refined_deg 1.621 r_mcbond_it 1.458 r_nbtor_refined 0.303 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.219 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.133 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 6061 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 130
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling