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Organophoshatedegrading enzyme (OpdA)-phosphate complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 0.4 M sodium potassium tartrate tetrahydrate pH 7.0., VAPOR DIFFUSION, HANGING DROP, temperature 18K, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.04 59.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.189 α = 90 b = 109.189 β = 90 c = 62.932 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 IMAGE PLATE RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 94.56 100 0.105 0.105 8.3 5.02 22261 26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 0.321 0.321 3.6 4.96 2200
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 2.2 41.24 21123 1136 99.97 0.17511 0.17203 0.1721 0.23341 0.2345 RANDOM 25.671
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] -0.15 -0.08 -0.15 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.336 r_dihedral_angle_4_deg 18.101 r_dihedral_angle_3_deg 14.528 r_dihedral_angle_1_deg 6.711 r_scangle_it 4.5 r_scbond_it 2.79 r_angle_refined_deg 1.77 r_mcangle_it 1.537 r_mcbond_it 0.852 r_metal_ion_refined 0.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.336 r_dihedral_angle_4_deg 18.101 r_dihedral_angle_3_deg 14.528 r_dihedral_angle_1_deg 6.711 r_scangle_it 4.5 r_scbond_it 2.79 r_angle_refined_deg 1.77 r_mcangle_it 1.537 r_mcbond_it 0.852 r_metal_ion_refined 0.495 r_symmetry_hbond_refined 0.315 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.111 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 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_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 2511 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 9
Software Software Software Name Purpose CrystalClear data collection REFMAC refinement CrystalClear data reduction CrystalClear data scaling