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Ntf2-like, potential transfer protein TraM from Gram-positive conjugative plasmid pIP501
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 7.33 298 1 mg/ml protein, 16.5% PEG 3350 (final concentration in drop v/v), 0.1 M Hepes, pH 7.33, microbatch under oil, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.73 28.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.21 α = 89.91 b = 54.98 β = 86.44 c = 93.47 γ = 78.63
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 225 mm CCD toroidal mirror (M2) to vertically and horizontally focus the beam at the sample position (with 2:1 horizontal demagnification) 2011-05-29 SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9792 SLS X06DA
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 2.5 50 97.5 0.116 14.91 52900 25885
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 97.7 0.48 4.05
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.5 46.89 52900 24589 1295 97.87 0.2118 0.20921 0.2099 0.26109 0.2596 RANDOM 28.803
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] 2.04 -0.92 0.8 -0.52 -0.04 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.369 r_dihedral_angle_3_deg 19.855 r_dihedral_angle_4_deg 15.12 r_dihedral_angle_1_deg 7.139 r_angle_refined_deg 1.762 r_chiral_restr 0.12 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.369 r_dihedral_angle_3_deg 19.855 r_dihedral_angle_4_deg 15.12 r_dihedral_angle_1_deg 7.139 r_angle_refined_deg 1.762 r_chiral_restr 0.12 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5412 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction