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OpdA from Agrobacterium radiobacter with bound inhibitor trimethyl phosphate at 1.8 A resolution
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 2.69 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.926 α = 90 b = 108.926 β = 90 c = 62.345 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 2004-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.8 20 97 39806 38568
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 1.8 1.86 97.3
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 1.8 19.6 36354 34612 1742 0.192 0.18946 0.18818 0.1815 0.2143 0.2111 RANDOM 15.65
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] -1 -0.5 -1 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.917 r_dihedral_angle_4_deg 14.226 r_dihedral_angle_3_deg 12.515 r_dihedral_angle_1_deg 5.981 r_scangle_it 3.397 r_scbond_it 2.172 r_angle_refined_deg 1.36 r_mcangle_it 1.104 r_mcbond_it 0.919 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.917 r_dihedral_angle_4_deg 14.226 r_dihedral_angle_3_deg 12.515 r_dihedral_angle_1_deg 5.981 r_scangle_it 3.397 r_scbond_it 2.172 r_angle_refined_deg 1.36 r_mcangle_it 1.104 r_mcbond_it 0.919 r_nbtor_refined 0.304 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.168 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2511 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing