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Structure of OpdA mutant (G60A/A80V/R118Q/K185R/Q206P/D208G/I260T/G273S)
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 59.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.156 α = 90 b = 109.156 β = 90 c = 62.692 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 ADSC QUANTUM 315r Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing) 2007-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97839 SSRL BL7-1
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 99.9 47531
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 99.1
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 1.7 40 45190 2316 99.89 0.17671 0.17573 0.1754 0.19615 0.1944 RANDOM 20.284
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] -0.83 -0.41 -0.83 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.552 r_dihedral_angle_4_deg 16.457 r_dihedral_angle_3_deg 13.182 r_dihedral_angle_1_deg 6.255 r_scangle_it 3.435 r_scbond_it 2.102 r_angle_refined_deg 1.43 r_mcangle_it 1.356 r_mcbond_it 0.827 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.552 r_dihedral_angle_4_deg 16.457 r_dihedral_angle_3_deg 13.182 r_dihedral_angle_1_deg 6.255 r_scangle_it 3.435 r_scbond_it 2.102 r_angle_refined_deg 1.43 r_mcangle_it 1.356 r_mcbond_it 0.827 r_nbtor_refined 0.309 r_nbd_refined 0.233 r_symmetry_hbond_refined 0.162 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.092 r_bond_refined_d 0.011 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 287 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing