☰ Navigation Tabs
Crystal structure of polyprenyl synthetase from pseudomonas fluorescens pf-5 complexed with magnesium and isoprenyl pyrophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LJI PDB ENTRY 3LJI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 0.1M SODIUM CACODYLATE, PH 6.5, 20% PEG 8K, 200MM MAGNESIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.362 α = 90 b = 48.362 β = 90 c = 208.592 γ = 120
Symmetry Space Group P 31 2 1
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 2010-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 1.76 40 97.2 0.088 6.3 5.2 29256 -5 23.078
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 1.76 1.79 78.8 0.69 1.5 4.8
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 PDB ENTRY 3LJI 1.76 20 27540 918 97.4 0.19476 0.19381 0.1954 0.22282 0.2198 RANDOM 34.746
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] -2.46 -1.23 -2.46 3.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.63 r_dihedral_angle_4_deg 17.257 r_dihedral_angle_3_deg 15.899 r_scangle_it 11.059 r_scbond_it 8.156 r_mcangle_it 5.421 r_dihedral_angle_1_deg 4.9 r_mcbond_it 3.896 r_angle_refined_deg 1.417 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.63 r_dihedral_angle_4_deg 17.257 r_dihedral_angle_3_deg 15.899 r_scangle_it 11.059 r_scbond_it 8.156 r_mcangle_it 5.421 r_dihedral_angle_1_deg 4.9 r_mcbond_it 3.896 r_angle_refined_deg 1.417 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2117 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 47
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction DENZO data reduction SCALEPACK data scaling