X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JKSPDB ENTRY 1JKS

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.2361.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.844α = 90
b = 62.336β = 90
c = 88.345γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
11.362.261000.08176.564311
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.371000.562.75.8

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 DIFFRACTIONMADTHROUGHOUTPDB ENTRY 1JKS1.388.3961052325799.80.1320.1310.159RANDOM11.97
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]
-1.250.530.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.686
r_dihedral_angle_4_deg18.88
r_dihedral_angle_3_deg14.173
r_dihedral_angle_1_deg6.223
r_scangle_it5.652
r_scbond_it3.924
r_mcangle_it2.928
r_mcbond_it2.004
r_angle_refined_deg1.874
r_angle_other_deg1.024
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.686
r_dihedral_angle_4_deg18.88
r_dihedral_angle_3_deg14.173
r_dihedral_angle_1_deg6.223
r_scangle_it5.652
r_scbond_it3.924
r_mcangle_it2.928
r_mcbond_it2.004
r_angle_refined_deg1.874
r_angle_other_deg1.024
r_chiral_restr0.125
r_bond_refined_d0.02
r_gen_planes_refined0.01
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2228
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing