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Crystal structure of the second and third fibronectin F1 modules in complex with a fragment of staphylococcus aureus fnbpa-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RKZ PDB ENTRY 2RKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.95M succinic acid, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.05 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.495 α = 90 b = 73.438 β = 95.05 c = 36.742 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 mirrors 2008-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97900 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 36.588 96.3 0.051 20.7 3.8 21298 19459 3.7 16.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.79 95.7 0.321 4.2 3.8 2952
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 2RKZ 1.7 36.588 3.7 21298 19459 1051 96.3 0.17865 0.17865 0.17656 0.1758 0.21665 0.2171 RANDOM 20.14
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] 0.79 -0.51 -0.75 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.103 r_dihedral_angle_4_deg 14.806 r_dihedral_angle_3_deg 13.072 r_dihedral_angle_1_deg 6.095 r_scangle_it 4.036 r_scbond_it 2.536 r_mcangle_it 1.792 r_angle_refined_deg 1.428 r_mcbond_it 1.034 r_symmetry_hbond_refined 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.103 r_dihedral_angle_4_deg 14.806 r_dihedral_angle_3_deg 13.072 r_dihedral_angle_1_deg 6.095 r_scangle_it 4.036 r_scbond_it 2.536 r_mcangle_it 1.792 r_angle_refined_deg 1.428 r_mcbond_it 1.034 r_symmetry_hbond_refined 0.39 r_nbtor_refined 0.318 r_nbd_refined 0.249 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.171 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_chiral_restr 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1636 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling PHASER phasing