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Methanobactin periplasmic binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 PEG3350, Bis-Tris, Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.82 56.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.2 α = 90 b = 141.5 β = 90 c = 83.1 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARMOSAIC 300 mm CCD 2015-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 1.9 50 100 0.17 22.93 14.79 56967
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3PAM 1.9 44.003 1.35 56958 2849 99.98 0.1584 0.1565 0.1576 0.1945 0.1951
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 f_dihedral_angle_d 12.996 f_angle_d 0.824 f_chiral_restr 0.054 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4496 Nucleic Acid Atoms Solvent Atoms 692 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling BALBES phasing