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Crystal structure of the Pseudomonas fluorescens agglutinin (PFA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S5V PDB entry 3S5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 1.0 M sodium citrate and 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.982 α = 90 b = 70.343 β = 111.73 c = 62.307 γ = 90
Symmetry Space Group C 1 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 93 IMAGE PLATE RIGAKU RAXIS IV++ 2010-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 28.14 93.8 26011 24397 1 2.1
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 1.7 1.76 90.6 0.294 2.4 1.9 2334
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3S5V 1.7 28.14 2.1 23411 22452 2531 95.9 0.18015 0.18015 0.17624 0.1896 0.21523 0.2247 RANDOM 38.737
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] 0.48 -0.73 -0.94 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.89 r_dihedral_angle_4_deg 11.178 r_dihedral_angle_3_deg 11.161 r_dihedral_angle_1_deg 6.67 r_scangle_it 2.281 r_scbond_it 1.583 r_angle_refined_deg 1.343 r_mcangle_it 1.067 r_mcbond_it 0.628 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.89 r_dihedral_angle_4_deg 11.178 r_dihedral_angle_3_deg 11.161 r_dihedral_angle_1_deg 6.67 r_scangle_it 2.281 r_scbond_it 1.583 r_angle_refined_deg 1.343 r_mcangle_it 1.067 r_mcbond_it 0.628 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1966 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling