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OpdA from Agrobacterium radiobacter with bound product dimethylthiophosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 277 20% PEG 3350, 0.2M NaNO3, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.71 54.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.956 α = 90 b = 108.956 β = 90 c = 62.672 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 173 IMAGE PLATE RIGAKU RAXIS IIC Confocal mirrors 2004-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5148
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 1.85 25 97.7 36889 35872
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 97.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.85 25 34142 32517 1625 0.174 0.16742 0.16613 0.1667 0.19367 0.1631 RANDOM 16.04
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] -0.96 -0.48 -0.96 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.758 r_dihedral_angle_4_deg 13.949 r_dihedral_angle_3_deg 12.743 r_dihedral_angle_1_deg 6.03 r_scangle_it 3.311 r_scbond_it 2.081 r_angle_refined_deg 1.3 r_mcangle_it 1.108 r_mcbond_it 0.72 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.758 r_dihedral_angle_4_deg 13.949 r_dihedral_angle_3_deg 12.743 r_dihedral_angle_1_deg 6.03 r_scangle_it 3.311 r_scbond_it 2.081 r_angle_refined_deg 1.3 r_mcangle_it 1.108 r_mcbond_it 0.72 r_nbtor_refined 0.303 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.182 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 2511 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing