X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5J5U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52771.5 M ammonium sulphate, 50 mM Tris-HCl pH 7.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.703α = 90
b = 140.269β = 90
c = 186.63γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002015-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.979APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.0256.9399.710.0850.0930.99711.136.217200835.74
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)
12.022.09499.990.5210.9142.276.2

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 REPLACEMENTTHROUGHOUT5J5U2.0256.93163616839298.690.15280.15160.1761RANDOM43.579
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]
0.98-0.45-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.058
r_sphericity_free31.514
r_sphericity_bonded16.714
r_dihedral_angle_4_deg16.359
r_dihedral_angle_3_deg12.013
r_dihedral_angle_1_deg5.851
r_angle_refined_deg0.921
r_angle_other_deg0.834
r_rigid_bond_restr0.704
r_chiral_restr0.047
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.058
r_sphericity_free31.514
r_sphericity_bonded16.714
r_dihedral_angle_4_deg16.359
r_dihedral_angle_3_deg12.013
r_dihedral_angle_1_deg5.851
r_angle_refined_deg0.921
r_angle_other_deg0.834
r_rigid_bond_restr0.704
r_chiral_restr0.047
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8220
Nucleic Acid Atoms
Solvent Atoms984
Heterogen Atoms184

Software

Software
Software NamePurpose
REFMACrefinement
xia2data scaling
PHASERphasing
PDB_EXTRACTdata extraction
xia2data reduction