X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MK5PDB entry 1MK5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.527738% saturated ammonium sulfate, 0.1 M sodium acetate, pH 4.5, 0.2 M sodium chloride, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1442.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.39α = 90
b = 93.811β = 90
c = 104.449γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IIMSINGLE WAVELENGTH
21x-ray100IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178
2SYNCHROTRONSSRL BEAMLINE BL11-10.98SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1,20.855095189859189859
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,20.850.8683

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONisomorphous with known structureFREE RPDB entry 1MK50.8510180225180225948590.20.15520.15620.1550.1736RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
2015612097
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.125
s_zero_chiral_vol0.089
s_similar_adp_cmpnt0.052
s_from_restr_planes0.0327
s_angle_d0.032
s_bond_d0.018
s_rigid_bond_adp_cmpnt0.007
s_similar_dist
s_anti_bump_dis_restr
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1798
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms82

Software

Software
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing