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OpdA from Agrobacterium radiobacter with bound slow substrate diethyl 4-methoxyphenyl phosphate (20h)- 1.7 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 59.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.695 α = 90 b = 108.695 β = 90 c = 62.649 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 2006-08-01 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 1.7 20 95.2 47163 44867
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.81 73.2
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 ENTRY 2D2J 1.7 18 47080 42685 2160 95.25 0.16627 0.16506 0.1648 0.19012 0.1889 RANDOM 18.275
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] -0.99 -0.5 -0.99 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.52 r_dihedral_angle_4_deg 14.233 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_1_deg 6.144 r_scangle_it 4.28 r_scbond_it 2.83 r_angle_refined_deg 1.649 r_mcangle_it 1.601 r_mcbond_it 1.165 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.52 r_dihedral_angle_4_deg 14.233 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_1_deg 6.144 r_scangle_it 4.28 r_scbond_it 2.83 r_angle_refined_deg 1.649 r_mcangle_it 1.601 r_mcbond_it 1.165 r_nbtor_refined 0.311 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.126 r_symmetry_hbond_refined 0.109 r_metal_ion_refined 0.049 r_bond_refined_d 0.022 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2527 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing