☰ Navigation Tabs
Crystal structure of human dehydrodolichyl diphosphate synthase (NgBR/DHDDS) in complex with Mg and IPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X06 1X06, 6JCN experimental model PDB 6JCN 1X06, 6JCN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 2.5 mM MgCl2, 3.3 mM IPP, 0.1 M Bicine, 10% v/v 2-propanol, 22% PEG 1500
Crystal Properties Matthews coefficient Solvent content 3.09 60.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.67 α = 90 b = 185.67 β = 90 c = 113.351 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 315 2019-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.306 40 99.2 0.108 0.113 0.032 7.5 12.8 31367
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 2.5 2.59 94.3 0.877 0.927 0.291 0.826 8.7
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 1X06, 6JCN 2.306 37.916 31367 1611 94.939 0.214 0.2123 0.2157 0.255 0.2579 72.717
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] -1.743 -0.871 -1.743 5.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.659 r_dihedral_angle_4_deg 19.542 r_dihedral_angle_3_deg 19.369 r_lrange_it 10.999 r_scangle_it 7.911 r_mcangle_it 6.966 r_dihedral_angle_1_deg 6.088 r_scbond_it 5.353 r_mcbond_it 4.63 r_angle_refined_deg 1.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.659 r_dihedral_angle_4_deg 19.542 r_dihedral_angle_3_deg 19.369 r_lrange_it 10.999 r_scangle_it 7.911 r_mcangle_it 6.966 r_dihedral_angle_1_deg 6.088 r_scbond_it 5.353 r_mcbond_it 4.63 r_angle_refined_deg 1.133 r_nbtor_refined 0.306 r_nbd_refined 0.219 r_symmetry_nbd_refined 0.212 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.131 r_chiral_restr 0.092 r_gen_planes_refined 0.005 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3900 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement DENZO data reduction HKL-2000 data scaling PHASER phasing