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Structure of OpdA Y257F mutant soaked with diethyl 4-methoxyphenyl phosphate for 20 hours.
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 6.5 291 14.4 % PEG 8000, 160mM calcium acetate hydrate, 80mM sodium cacodylate, 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.98 58.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109 α = 90 b = 109 β = 90 c = 62 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 IV++ Mirrors 2008-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.89 50 100 0.051 22.6 7.97 33015 33015
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 1.89 50 100
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 2D2J 1.89 17.27 33015 33015 1676 95.91 0.15673 0.15673 0.15478 0.1562 0.19493 0.1954 RANDOM 17.278
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.13 r_dihedral_angle_4_deg 15.988 r_dihedral_angle_3_deg 12.307 r_dihedral_angle_1_deg 6.047 r_scangle_it 3.162 r_scbond_it 1.975 r_angle_refined_deg 1.377 r_mcangle_it 1.107 r_mcbond_it 0.711 r_symmetry_hbond_refined 0.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.13 r_dihedral_angle_4_deg 15.988 r_dihedral_angle_3_deg 12.307 r_dihedral_angle_1_deg 6.047 r_scangle_it 3.162 r_scbond_it 1.975 r_angle_refined_deg 1.377 r_mcangle_it 1.107 r_mcbond_it 0.711 r_symmetry_hbond_refined 0.438 r_nbtor_refined 0.307 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.103 r_metal_ion_refined 0.029 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2509 Nucleic Acid Atoms Solvent Atoms 444 Heterogen Atoms 19
Software Software Software Name Purpose CrystalClear data collection REFMAC refinement CrystalClear data reduction CrystalClear data scaling