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CRYSTAL STRUCTURE OF DODECAPRENYL DIPHOSPHATE SYNTHASE FROM THERMOBIFIDA FUSCA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 0.1 M citric acid sodium citrate, 5% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.1 41.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.862 α = 90 b = 137.59 β = 90 c = 168.854 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 270 2007-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1 Photon Factory BL-17A
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 2.6 49.409 99.8 0.056 46.201 7.3 52305
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 2.6 2.69 100 0.371 5.124 7.3
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 1F75 2.6 49.409 51548 2479 99.833 0.191 0.189 0.1891 0.2336 0.2335 63.085
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] 1.996 -2.748 0.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.606 r_dihedral_angle_4_deg 17.774 r_dihedral_angle_3_deg 15.467 r_lrange_other 11.27 r_lrange_it 11.267 r_scangle_it 8.527 r_scangle_other 8.525 r_mcangle_other 7.88 r_mcangle_it 7.879 r_dihedral_angle_1_deg 5.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.606 r_dihedral_angle_4_deg 17.774 r_dihedral_angle_3_deg 15.467 r_lrange_other 11.27 r_lrange_it 11.267 r_scangle_it 8.527 r_scangle_other 8.525 r_mcangle_other 7.88 r_mcangle_it 7.879 r_dihedral_angle_1_deg 5.902 r_scbond_it 5.602 r_scbond_other 5.602 r_mcbond_it 5.471 r_mcbond_other 5.468 r_angle_other_deg 2.315 r_angle_refined_deg 1.369 r_symmetry_xyhbond_nbd_refined 0.248 r_symmetry_nbd_refined 0.246 r_nbd_other 0.222 r_symmetry_nbd_other 0.22 r_nbd_refined 0.2 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.137 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.06 r_bond_other_d 0.035 r_gen_planes_other 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11544 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing