X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP300Protein solution: 12.0 mg/ml, 0.01 M Tris-HCl pH 8.3, and 10/mg/ml tryptone Crystallization condition: Classics II (Qiagen) D10: 0.1 M Bis-Tris pH 6.5 and 20% (w/v) PEG 5000 MME
Crystal Properties
Matthews coefficientSolvent content
2.2344.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.277α = 90
b = 74.63β = 109.38
c = 155.061γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2016-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.978APS21-ID-D

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
11.853098.40.10817.33.292580
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8899.20.6180.582.33

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 REPLACEMENTTHROUGHOUT4FAJ1.853087975460497.040.169140.167260.20489RANDOM21.565
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]
-0.42-0.070.080.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.719
r_dihedral_angle_3_deg12.337
r_dihedral_angle_4_deg10.962
r_dihedral_angle_1_deg5.907
r_long_range_B_refined5.258
r_long_range_B_other5.258
r_angle_refined_deg1.321
r_scangle_other1.199
r_mcangle_it0.932
r_mcangle_other0.932
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.719
r_dihedral_angle_3_deg12.337
r_dihedral_angle_4_deg10.962
r_dihedral_angle_1_deg5.907
r_long_range_B_refined5.258
r_long_range_B_other5.258
r_angle_refined_deg1.321
r_scangle_other1.199
r_mcangle_it0.932
r_mcangle_other0.932
r_angle_other_deg0.892
r_scbond_it0.723
r_scbond_other0.723
r_mcbond_it0.551
r_mcbond_other0.55
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8236
Nucleic Acid Atoms
Solvent Atoms1113
Heterogen Atoms

Software

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