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OpdA from Agrobacterium radiobacter with bound product diethyl thiophosphate from co-crystallisation with tetraethyl dithiopyrophosphate- 1.8 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 20% PEG 3350, 0.2M sodium nitrate, pH7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.02 59.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.876 α = 90 b = 108.876 β = 90 c = 62.839 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 IIC Confocal Mirrors 2006-05-03 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 95.8 40072 38340
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.91 94.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY2D2J 1.8 20 40005 36530 1807 95.83 0.16362 0.16208 0.1621 0.19505 0.1927 RANDOM 18.562
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] -1.03 -0.52 -1.03 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.37 r_dihedral_angle_4_deg 16.239 r_dihedral_angle_3_deg 12.965 r_dihedral_angle_1_deg 6.793 r_scangle_it 5.694 r_scbond_it 4.121 r_mcangle_it 2.511 r_mcbond_it 2.04 r_angle_refined_deg 1.618 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.37 r_dihedral_angle_4_deg 16.239 r_dihedral_angle_3_deg 12.965 r_dihedral_angle_1_deg 6.793 r_scangle_it 5.694 r_scbond_it 4.121 r_mcangle_it 2.511 r_mcbond_it 2.04 r_angle_refined_deg 1.618 r_nbtor_refined 0.311 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.195 r_chiral_restr 0.151 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.097 r_metal_ion_refined 0.036 r_bond_refined_d 0.021 r_gen_planes_refined 0.018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2506 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing