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OpdA from Agrobacterium radiobacter with bound product diethyl phosphate from crystal soaking with diethyl 4-methoxyphenyl phosphate (450h)- 2.5 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 2.99 58.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.096 α = 90 b = 109.096 β = 90 c = 61.88 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 2006-08-25 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 2.5 20 96 14998 14351
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.66 82.5
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 (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 PDB ENTRY 2D2J 2.5 20 14942 13620 717 95.95 0.15868 0.15868 0.15526 0.1553 0.2252 0.2249 RANDOM 32.041
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] -1.87 -0.93 -1.87 2.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.068 r_dihedral_angle_4_deg 23.02 r_dihedral_angle_3_deg 17.463 r_dihedral_angle_1_deg 8.367 r_scangle_it 7.841 r_scbond_it 5.621 r_mcangle_it 3.306 r_mcbond_it 2.201 r_angle_refined_deg 1.653 r_nbtor_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.068 r_dihedral_angle_4_deg 23.02 r_dihedral_angle_3_deg 17.463 r_dihedral_angle_1_deg 8.367 r_scangle_it 7.841 r_scbond_it 5.621 r_mcangle_it 3.306 r_mcbond_it 2.201 r_angle_refined_deg 1.653 r_nbtor_refined 0.329 r_nbd_refined 0.26 r_xyhbond_nbd_refined 0.196 r_symmetry_vdw_refined 0.172 r_symmetry_hbond_refined 0.137 r_chiral_restr 0.135 r_gen_planes_refined 0.021 r_bond_refined_d 0.02 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 2504 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing