7QF5

Structure of the Q103L mutant of miniSOG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GPU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293100 mM Tris-Hcl pH 8.0, 20 mM MgCl2, 28% PEG 4000, 15 mM CoCl2
Crystal Properties
Matthews coefficientSolvent content
2.0640.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.05α = 90
b = 40.05β = 90
c = 134.26γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MTOROIDAL MIRROR2015-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9789ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.3738.3899.90.06123.98.32397921.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.371.411.070.6432.1

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-VALUE6GPU1.3738.37923979115299.9370.1280.12570.173917.635
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]
0.0760.076-0.152
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.885
r_dihedral_angle_4_deg19.202
r_dihedral_angle_3_deg12.602
r_dihedral_angle_1_deg6.562
r_lrange_it3.634
r_lrange_other3.366
r_scangle_it2.665
r_scangle_other2.663
r_scbond_other2.17
r_scbond_it2.164
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.885
r_dihedral_angle_4_deg19.202
r_dihedral_angle_3_deg12.602
r_dihedral_angle_1_deg6.562
r_lrange_it3.634
r_lrange_other3.366
r_scangle_it2.665
r_scangle_other2.663
r_scbond_other2.17
r_scbond_it2.164
r_mcangle_other2.008
r_mcangle_it1.997
r_rigid_bond_restr1.817
r_angle_refined_deg1.62
r_mcbond_it1.587
r_mcbond_other1.475
r_angle_other_deg1.382
r_symmetry_xyhbond_nbd_refined0.254
r_nbd_refined0.239
r_xyhbond_nbd_refined0.219
r_symmetry_nbd_refined0.217
r_nbd_other0.188
r_symmetry_nbd_other0.186
r_nbtor_refined0.178
r_chiral_restr0.091
r_symmetry_nbtor_other0.082
r_symmetry_xyhbond_nbd_other0.031
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_metal_ion_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms938
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing