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Structure of the Bifunctional IspDF from Campylobacter jejuni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I52 PDB ENTRIES 1I52 AND 1GX1 experimental model PDB 1GX1 PDB ENTRIES 1I52 AND 1GX1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 35 % ETHYLENE GLYCOL
Crystal Properties Matthews coefficient Solvent content 3.3 62.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.758 α = 90 b = 108.758 β = 90 c = 161.262 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 160 CCD ADSC CCD TOROIDAL MIRROR 2002-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.3 14.96 98.4 0.07 41.5 19.4 489834 43.8
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 2.3 2.38 87.2 0.36 5.3
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 (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 ENTRIES 1I52 AND 1GX1 2.3 14.96 489834 1278 98.4 0.17 0.167 0.1772 0.222 0.2263 RANDOM 37.69
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] 0.099 0.05 0.099 -0.149
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.217 r_scbond_it 3.844 r_mcangle_it 2.629 r_angle_refined_deg 1.744 r_mcbond_it 1.442 r_angle_other_deg 0.989 r_symmetry_vdw_other 0.349 r_symmetry_hbond_refined 0.291 r_nbd_other 0.259 r_symmetry_vdw_refined 0.23
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.217 r_scbond_it 3.844 r_mcangle_it 2.629 r_angle_refined_deg 1.744 r_mcbond_it 1.442 r_angle_other_deg 0.989 r_symmetry_vdw_other 0.349 r_symmetry_hbond_refined 0.291 r_nbd_other 0.259 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.195 r_nbtor_refined 0.182 r_chiral_restr 0.148 r_nbtor_other 0.092 r_bond_refined_d 0.031 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.003 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2914 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing