6NL7

Crystal structure of B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29880 mM acetic acid pH 3.6, 20 mM acetic acid pH 5.8, 30% 2,4-methylpentanediol, 200 mM NaCl and 20 mM zinc sulfate
Crystal Properties
Matthews coefficientSolvent content
2.6753.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.903α = 90
b = 63.057β = 103.31
c = 53.225γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2018-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.098ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.451.890.030.17.89.944547
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.3981.43425.89

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1PGA1.440.0644547231790.030.115110.11290.15813RANDOM19.862
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]
0.13-0.4-0.050.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.856
r_sphericity_free31.361
r_sphericity_bonded18.116
r_dihedral_angle_3_deg13.618
r_dihedral_angle_4_deg9.851
r_dihedral_angle_1_deg5.961
r_long_range_B_refined5.758
r_long_range_B_other5.272
r_scangle_other5.125
r_scbond_it4.563
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.856
r_sphericity_free31.361
r_sphericity_bonded18.116
r_dihedral_angle_3_deg13.618
r_dihedral_angle_4_deg9.851
r_dihedral_angle_1_deg5.961
r_long_range_B_refined5.758
r_long_range_B_other5.272
r_scangle_other5.125
r_scbond_it4.563
r_scbond_other4.486
r_rigid_bond_restr3.788
r_mcangle_it2.747
r_mcangle_other2.747
r_mcbond_it2.182
r_mcbond_other2.157
r_angle_refined_deg1.85
r_angle_other_deg1.059
r_chiral_restr0.1
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1764
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing