X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SG1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7295Protein: 8.2 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (B4), 0.01M MIB buffer (pH 7.0), 25% (w/v) PEG 1500.
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.243α = 90
b = 80.13β = 95.76
c = 126.511γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2017-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rpim I (All)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
12301000.0760.0760.0418.94.5113220-330.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.031000.7560.7560.4050.6972.034.4

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 REPLACEMENTTHROUGHOUT3SG1229.29107143583399.730.224570.222250.26625RANDOM50.996
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]
2.30.14-2.21-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.214
r_dihedral_angle_4_deg14.977
r_dihedral_angle_3_deg11.922
r_long_range_B_other9.523
r_long_range_B_refined9.517
r_scangle_other7.067
r_mcangle_it6.767
r_mcangle_other6.767
r_mcbond_other4.808
r_mcbond_it4.807
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.214
r_dihedral_angle_4_deg14.977
r_dihedral_angle_3_deg11.922
r_long_range_B_other9.523
r_long_range_B_refined9.517
r_scangle_other7.067
r_mcangle_it6.767
r_mcangle_other6.767
r_mcbond_other4.808
r_mcbond_it4.807
r_scbond_it4.719
r_scbond_other4.719
r_dihedral_angle_1_deg3.036
r_angle_refined_deg1.518
r_angle_other_deg0.886
r_chiral_restr0.088
r_gen_planes_refined0.022
r_gen_planes_other0.02
r_bond_refined_d0.01
r_bond_other_d0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12687
Nucleic Acid Atoms
Solvent Atoms637
Heterogen Atoms220

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing