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Crystal structure of the protein secretion chaperone CsaA from Agrobacterium tumefaciens with a genetically fused phage-display derived peptide substrate at the N-terminus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GD7 pdb entry 1gd7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 292 30% PEG 4000, 0.4 M ammonium acetate, 0.1 M sodium citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.15 42.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.528 α = 90 b = 60.528 β = 90 c = 115.247 γ = 120
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 VariMax Cu HF 2006-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 1.65 23.86 89.4 0.039 30 5.71 25681 25681 5 5
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 1.65 1.71 49.7 0.162 8.6 4.47 1427
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1gd7 1.65 23.86 25680 25680 1301 89.38 0.161 0.161 0.16 0.173 0.1995 RANDOM 8.236
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.742 r_dihedral_angle_4_deg 18.172 r_dihedral_angle_3_deg 12.237 r_dihedral_angle_1_deg 6.282 r_scangle_it 1.663 r_angle_refined_deg 1.183 r_scbond_it 1.155 r_mcangle_it 0.693 r_mcbond_it 0.446 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.742 r_dihedral_angle_4_deg 18.172 r_dihedral_angle_3_deg 12.237 r_dihedral_angle_1_deg 6.282 r_scangle_it 1.663 r_angle_refined_deg 1.183 r_scbond_it 1.155 r_mcangle_it 0.693 r_mcbond_it 0.446 r_nbtor_refined 0.31 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.096 r_chiral_restr 0.084 r_symmetry_hbond_refined 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1696 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 21
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction PHASER phasing