6GPU

Crystal structure of miniSOG at 1.17A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EEP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293100 mM Tris-Hcl pH 8.0, 20 mM MgCl2, 28% PEG 4000, 0 or 15 mM CoCl2
Crystal Properties
Matthews coefficientSolvent content
2.0239.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.02α = 90
b = 40.02β = 90
c = 134.29γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9763ESRFID23-1

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
11.178099.80.062122.18.23791316.235
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)
11.171.299.91.2050.70428

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 REPLACEMENTTHROUGHOUT4eep1.1738.3536063185099.80.134140.132650.164RANDOM15.17
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]
0.020.02-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.962
r_sphericity_free23.7
r_dihedral_angle_4_deg20.15
r_dihedral_angle_3_deg13.176
r_sphericity_bonded8.426
r_dihedral_angle_1_deg6.195
r_long_range_B_refined3.792
r_long_range_B_other3.791
r_scangle_other2.34
r_scbond_other1.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.962
r_sphericity_free23.7
r_dihedral_angle_4_deg20.15
r_dihedral_angle_3_deg13.176
r_sphericity_bonded8.426
r_dihedral_angle_1_deg6.195
r_long_range_B_refined3.792
r_long_range_B_other3.791
r_scangle_other2.34
r_scbond_other1.89
r_scbond_it1.887
r_mcangle_other1.882
r_mcangle_it1.88
r_rigid_bond_restr1.797
r_angle_refined_deg1.7
r_mcbond_it1.45
r_mcbond_other1.411
r_angle_other_deg0.834
r_chiral_restr0.108
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms932
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms42

Software

Software
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
Cootmodel building