X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5C8Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293ammonium phosphate, imidazole, potassium chloride
Crystal Properties
Matthews coefficientSolvent content
3.0860.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.66α = 90
b = 90.17β = 90
c = 113.52γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.97916SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim 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
11.72113.521000.210.10.9951910.782387
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.760.6320.30.947

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 REPLACEMENTTHROUGHOUT5c8z1.723578020422899.950.142520.141380.16363RANDOM13.306
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]
-0.820.630.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.53
r_dihedral_angle_3_deg12.185
r_dihedral_angle_4_deg10.72
r_dihedral_angle_1_deg6.471
r_long_range_B_refined5.822
r_long_range_B_other5.714
r_scangle_other4.236
r_scbond_other2.932
r_scbond_it2.931
r_mcangle_other2.027
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.53
r_dihedral_angle_3_deg12.185
r_dihedral_angle_4_deg10.72
r_dihedral_angle_1_deg6.471
r_long_range_B_refined5.822
r_long_range_B_other5.714
r_scangle_other4.236
r_scbond_other2.932
r_scbond_it2.931
r_mcangle_other2.027
r_mcangle_it2.026
r_angle_refined_deg1.797
r_angle_other_deg1.607
r_mcbond_it1.404
r_mcbond_other1.399
r_chiral_restr0.107
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms4110
Nucleic Acid Atoms
Solvent Atoms480
Heterogen Atoms96

Software

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