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Crystal structure of thermophilic phosphotriesterase from Geobacillus kaustophilus HTA426
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F4D PDB ENTRY 3F4D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 291 0.1M HEPES pH7.6 12% w/v PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.76 55.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.321 α = 90 b = 88.877 β = 98.58 c = 89.384 γ = 90
Symmetry Space Group P 1 21 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 2009-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 95 29732
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 3F4D 2.4 47.15 28376 1502 96.2 0.19968 0.19606 0.1986 0.268 0.2682 RANDOM 40.72
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 -1.39 2.73 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.101 r_dihedral_angle_4_deg 23.48 r_dihedral_angle_3_deg 20.249 r_dihedral_angle_1_deg 8.506 r_scangle_it 5.45 r_scbond_it 3.755 r_angle_refined_deg 2.359 r_mcangle_it 2.229 r_mcbond_it 1.386 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.101 r_dihedral_angle_4_deg 23.48 r_dihedral_angle_3_deg 20.249 r_dihedral_angle_1_deg 8.506 r_scangle_it 5.45 r_scbond_it 3.755 r_angle_refined_deg 2.359 r_mcangle_it 2.229 r_mcbond_it 1.386 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.294 r_nbd_refined 0.24 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.165 r_bond_refined_d 0.03 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 5096 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 4
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling