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CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH BPH-981
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WJK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.3M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1M TRIS-HCL, 24%(W/V) POLYETHYLENE GLYCOL 3350
Crystal Properties Matthews coefficient Solvent content 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.032 α = 90 b = 111.999 β = 90 c = 133.822 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 315r 2012-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
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 2.5 25 100 0.097 9.4 5.8 49730
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 2.5 2.59 100 0.495 5.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3WJK 2.5 25 47239 2427 99.63 0.18931 0.18544 0.1902 0.26405 0.262 RANDOM 41.108
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] 0.21 1.3 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.367 r_dihedral_angle_4_deg 23.383 r_dihedral_angle_3_deg 22.361 r_long_range_B_other 9.596 r_long_range_B_refined 9.593 r_scangle_other 6.611 r_dihedral_angle_1_deg 5.756 r_mcangle_it 5.464 r_mcangle_other 5.464 r_scbond_it 4.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.367 r_dihedral_angle_4_deg 23.383 r_dihedral_angle_3_deg 22.361 r_long_range_B_other 9.596 r_long_range_B_refined 9.593 r_scangle_other 6.611 r_dihedral_angle_1_deg 5.756 r_mcangle_it 5.464 r_mcangle_other 5.464 r_scbond_it 4.438 r_scbond_other 4.436 r_mcbond_it 3.708 r_mcbond_other 3.707 r_angle_refined_deg 1.49 r_angle_other_deg 0.91 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 9411 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing