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IspH in complex with pyridin-2-ylmethyl diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 0.1 M BIS-TRIS, 0.2 M ammonium sulfate, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.47 α = 90 b = 80.8 β = 90 c = 111.49 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 PIXEL PSI PILATUS 6M 2012-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 30 98.7 0.09 11.37 6.9 50202 49549 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 95.6 0.421 2.82
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 3KE8 1.9 14.97 47666 49441 2472 98.5 0.22 0.218 0.256 0.2654 36.53
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] -3.43 3.32 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.244 r_sphericity_free 29.692 r_dihedral_angle_4_deg 17.198 r_sphericity_bonded 16.279 r_dihedral_angle_3_deg 14.491 r_dihedral_angle_1_deg 5.455 r_rigid_bond_restr 4.974 r_mcangle_it 1.712 r_angle_refined_deg 1.399 r_mcbond_it 0.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.244 r_sphericity_free 29.692 r_dihedral_angle_4_deg 17.198 r_sphericity_bonded 16.279 r_dihedral_angle_3_deg 14.491 r_dihedral_angle_1_deg 5.455 r_rigid_bond_restr 4.974 r_mcangle_it 1.712 r_angle_refined_deg 1.399 r_mcbond_it 0.985 r_mcbond_other 0.983 r_angle_other_deg 0.744 r_chiral_restr 0.095 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4773 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 46
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing