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OpdA from Agrobacterium radiobacter with bound diethyl thiophosphate from crystal soaking with the compound- 1.95 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D2J PDB ENTRY 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 3.01 59.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.923 α = 90 b = 108.923 β = 90 c = 62.647 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 2006-10-24 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 1.95 20 99.3 31547 31298
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2.07 96.3
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 ENTRY 2D2J 1.95 20 31477 29774 1502 99.36 0.15604 0.15403 0.1562 0.19654 0.1987 RANDOM 20.31
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] -1.16 -0.58 -1.16 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.477 r_dihedral_angle_4_deg 17.01 r_dihedral_angle_3_deg 14.029 r_dihedral_angle_1_deg 7.11 r_scangle_it 6.957 r_scbond_it 5.008 r_mcangle_it 2.816 r_mcbond_it 2.344 r_angle_refined_deg 1.638 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.477 r_dihedral_angle_4_deg 17.01 r_dihedral_angle_3_deg 14.029 r_dihedral_angle_1_deg 7.11 r_scangle_it 6.957 r_scbond_it 5.008 r_mcangle_it 2.816 r_mcbond_it 2.344 r_angle_refined_deg 1.638 r_nbtor_refined 0.311 r_nbd_refined 0.236 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.149 r_symmetry_hbond_refined 0.102 r_metal_ion_refined 0.044 r_bond_refined_d 0.022 r_gen_planes_refined 0.019 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 272 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing