X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XCY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320% Peg 3350, 0.2m K formate
Crystal Properties
Matthews coefficientSolvent content
2.2244.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.45α = 90
b = 74.01β = 90
c = 160.69γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173PIXELDECTRIS PILATUS 6M-F2019-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91188DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
10.9947.7398.50.9998.95.4405311
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)
10.991.0189.60.6890.71

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 REPLACEMENTTHROUGHOUT2xcy0.9947.733852211994698.490.21920.2180.2407RANDOM12.478
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]
0.27-0.690.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.263
r_sphericity_free24.228
r_dihedral_angle_4_deg17.441
r_sphericity_bonded15.034
r_dihedral_angle_3_deg11.097
r_dihedral_angle_1_deg7.164
r_rigid_bond_restr5.798
r_angle_refined_deg1.614
r_angle_other_deg0.85
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.263
r_sphericity_free24.228
r_dihedral_angle_4_deg17.441
r_sphericity_bonded15.034
r_dihedral_angle_3_deg11.097
r_dihedral_angle_1_deg7.164
r_rigid_bond_restr5.798
r_angle_refined_deg1.614
r_angle_other_deg0.85
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.006
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5857
Nucleic Acid Atoms
Solvent Atoms900
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing