☰ Navigation Tabs
Structure of OpdA mutant (G60A/A80V/S92A/R118Q/K185R/Q206P/D208G/I260T/G273S) with diethyl 4-methoxyphenyl phosphate bound in the active site
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% PEG3350, 0.2M NaNO3, pH7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.02 59.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.011 α = 90 b = 109.011 β = 90 c = 62.689 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 CCD MARMOSAIC 325 mm CCD flat collimating mirror, double crystal monochromator, toroid focusing mirror 2007-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.975 SSRL BL9-2
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 40 92.4 43843 43843
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 1.76 51.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1.85 29.8 34885 1715 99.21 0.17569 0.17404 0.1747 0.20883 0.2083 RANDOM 25
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] -1.31 -0.65 -1.31 1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.921 r_dihedral_angle_4_deg 18.385 r_dihedral_angle_3_deg 15.315 r_dihedral_angle_1_deg 6.888 r_scangle_it 4.066 r_scbond_it 2.494 r_angle_refined_deg 1.624 r_mcangle_it 1.621 r_mcbond_it 1.008 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.921 r_dihedral_angle_4_deg 18.385 r_dihedral_angle_3_deg 15.315 r_dihedral_angle_1_deg 6.888 r_scangle_it 4.066 r_scbond_it 2.494 r_angle_refined_deg 1.624 r_mcangle_it 1.621 r_mcbond_it 1.008 r_nbtor_refined 0.305 r_nbd_refined 0.238 r_symmetry_hbond_refined 0.236 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 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 2520 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing