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Crystal structure of (R)-DHPS dehydrogenase HpsO from Ruegeria pomeroyi DSS-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LE3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293 0.8 M Sodium formate, 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.19 43.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.14 α = 96.27 b = 56.156 β = 105.96 c = 76.185 γ = 90.7
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 PILATUS 6M 2014-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9791 SSRF BL18U1
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 1.7 41.95 95.8 0.139 17.6 3.4 93413
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 1.7 1.73 93.9 0.356 4.5 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 FREE R-VALUE 1.7 41.95 88739 4672 95.71 0.15906 0.1572 0.19412 0.2048 RANDOM 19.017
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] 0.01 0.09 0.06 0.01 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.175 r_dihedral_angle_4_deg 18.087 r_dihedral_angle_3_deg 14.314 r_dihedral_angle_1_deg 6.562 r_long_range_B_refined 6.492 r_long_range_B_other 6.133 r_scangle_other 4.447 r_scbond_it 3.029 r_scbond_other 3.029 r_mcangle_it 2.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.175 r_dihedral_angle_4_deg 18.087 r_dihedral_angle_3_deg 14.314 r_dihedral_angle_1_deg 6.562 r_long_range_B_refined 6.492 r_long_range_B_other 6.133 r_scangle_other 4.447 r_scbond_it 3.029 r_scbond_other 3.029 r_mcangle_it 2.499 r_mcangle_other 2.498 r_angle_refined_deg 2.124 r_mcbond_it 1.8 r_mcbond_other 1.8 r_angle_other_deg 1.059 r_chiral_restr 0.176 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7363 Nucleic Acid Atoms Solvent Atoms 1120 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing