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Crystal structure of the Escherichia coli twin arginine leader peptide binding protein DmsD in a monomeric form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 1.25M ammonium sulfate, 12% glycerol, 0.1M Bis-Tris pH 6.5, 72 hours, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.9 68.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.02 α = 90 b = 128.02 β = 90 c = 78.723 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++ Rigaku VariMAX HF 2007-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.01 30.75 97.7 0.089 5.72 49796 48639 2 2 92.8
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 2.01 2.08 95.6 0.362 4.5 5.58 4703
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 THROUGHOUT 1s9u 2.01 30.75 49796 48639 2463 97.7 0.236 0.18 0.178 0.1795 0.213 0.2117 RANDOM 22.692
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] 0.43 0.22 0.43 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.863 r_dihedral_angle_4_deg 18.4 r_dihedral_angle_3_deg 12.736 r_dihedral_angle_1_deg 4.644 r_scangle_it 1.583 r_angle_refined_deg 1.036 r_scbond_it 1.02 r_mcangle_it 0.554 r_nbtor_refined 0.316 r_mcbond_it 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.863 r_dihedral_angle_4_deg 18.4 r_dihedral_angle_3_deg 12.736 r_dihedral_angle_1_deg 4.644 r_scangle_it 1.583 r_angle_refined_deg 1.036 r_scbond_it 1.02 r_mcangle_it 0.554 r_nbtor_refined 0.316 r_mcbond_it 0.312 r_symmetry_hbond_refined 0.244 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3345 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 75
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction PHASER phasing