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Crystal structure of the second and third fibronectin f1 modules in complex with a fragment of staphylococcus aureus fnbpa-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other A previous lower resolution structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.8M SUCCINIC ACID, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.08 60.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.59 α = 90 b = 109.72 β = 96.94 c = 71.47 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315 Liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror 2006-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97620 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 26.038 99.9 0.1 0.1 11.5 3.6 61539 58424 3.7 19.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.11 100 0.272 0.272 4.2 3.7 8970
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 A previous lower resolution structure 2 25.58 61510 58424 3086 99.97 0.2 0.2 0.197 0.261 0.2678 RANDOM 24.358
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] 3.64 -0.13 -2.17 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.418 r_dihedral_angle_1_deg 23.122 r_dihedral_angle_4_deg 18.765 r_dihedral_angle_3_deg 16.566 r_scangle_it 9.292 r_scbond_it 6.619 r_mcangle_it 4.349 r_mcbond_it 3.106 r_angle_refined_deg 1.423 r_symmetry_hbond_refined 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.418 r_dihedral_angle_1_deg 23.122 r_dihedral_angle_4_deg 18.765 r_dihedral_angle_3_deg 16.566 r_scangle_it 9.292 r_scbond_it 6.619 r_mcangle_it 4.349 r_mcbond_it 3.106 r_angle_refined_deg 1.423 r_symmetry_hbond_refined 0.35 r_nbtor_refined 0.338 r_nbd_refined 0.31 r_symmetry_vdw_refined 0.288 r_xyhbond_nbd_refined 0.228 r_chiral_restr 0.028 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5078 Nucleic Acid Atoms Solvent Atoms 822 Heterogen Atoms 28
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction PHASER phasing