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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 5 293 0.1 M citric acid sodium citrate pH 5.0, 0.7 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.15 42.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.095 α = 90 b = 137.878 β = 90 c = 168.652 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 2009-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 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 2.28 47.534 100 0.059 63.647 8.4 77502
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 2.28 2.32 100 0.385 8.564 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 2.28 47.534 76311 3830 99.877 0.205 0.2028 0.203 0.2394 0.2395 53.909
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] 0.595 -0.417 -0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.031 r_dihedral_angle_4_deg 17.237 r_dihedral_angle_3_deg 15.27 r_lrange_it 10.836 r_lrange_other 10.836 r_scangle_it 8.247 r_scangle_other 8.2 r_mcangle_other 7.009 r_mcangle_it 7.008 r_dihedral_angle_1_deg 5.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.031 r_dihedral_angle_4_deg 17.237 r_dihedral_angle_3_deg 15.27 r_lrange_it 10.836 r_lrange_other 10.836 r_scangle_it 8.247 r_scangle_other 8.2 r_mcangle_other 7.009 r_mcangle_it 7.008 r_dihedral_angle_1_deg 5.784 r_scbond_it 5.464 r_scbond_other 5.374 r_mcbond_it 4.933 r_mcbond_other 4.928 r_angle_other_deg 2.309 r_angle_refined_deg 1.41 r_symmetry_nbd_refined 0.227 r_nbd_other 0.226 r_symmetry_nbd_other 0.216 r_symmetry_xyhbond_nbd_refined 0.207 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.163 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.07 r_bond_other_d 0.035 r_gen_planes_other 0.013 r_symmetry_xyhbond_nbd_other 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11068 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling MOLREP phasing