7QHV

Crystal structure of the sulfoquinovosyl binding protein SmoF complexed with sulfoquinovosyl diacylglycerol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7QHUD_1292119394

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72790.2M L-Na-glutamate, alanine, glycine, lysine hydrochloride, serine, 0.1M TRIS, bicine, 12.5% MPD, PEG1000, PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.243.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.215α = 90
b = 69.589β = 91.539
c = 104.574γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray210PIXELDECTRIS PILATUS 6M-F2019-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97933DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.1469.5999.90.0930.1240.0810.9928.94.142301
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.142.20.3050.4060.2650.9424.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUED_12921193942.1457.99542277212499.8650.2060.20350.259824.287
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]
3.1243.128-0.769-2.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.392
r_dihedral_angle_4_deg22.688
r_dihedral_angle_3_deg14.801
r_dihedral_angle_1_deg6.61
r_lrange_it4.222
r_lrange_other4.204
r_scangle_it2.884
r_scangle_other2.883
r_mcangle_it2.553
r_mcangle_other2.553
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.392
r_dihedral_angle_4_deg22.688
r_dihedral_angle_3_deg14.801
r_dihedral_angle_1_deg6.61
r_lrange_it4.222
r_lrange_other4.204
r_scangle_it2.884
r_scangle_other2.883
r_mcangle_it2.553
r_mcangle_other2.553
r_scbond_it1.887
r_scbond_other1.885
r_mcbond_other1.677
r_mcbond_it1.676
r_angle_refined_deg1.504
r_angle_other_deg1.3
r_symmetry_xyhbond_nbd_refined0.214
r_nbd_refined0.201
r_symmetry_nbd_other0.179
r_nbd_other0.173
r_nbtor_refined0.165
r_xyhbond_nbd_refined0.155
r_symmetry_nbd_refined0.111
r_symmetry_nbtor_other0.078
r_chiral_restr0.069
r_symmetry_xyhbond_nbd_other0.043
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5828
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
MOLREPphasing