X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729360% saturated ammonium sulfate, 5% isopropanol (30% glycerol cryoprotectant), pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1643.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.611α = 90
b = 94.114β = 90
c = 104.595γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2009-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

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
11.2227.91999.80.12123.06513.46844868448
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)
11.221.2698.40.613106663

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1MK51.2227.9196497564975346899.680.12940.12940.12830.1506RANDOM14.95
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]
0.441.57-2.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.421
r_dihedral_angle_3_deg10.738
r_dihedral_angle_4_deg10.651
r_dihedral_angle_1_deg6.762
r_scangle_it4.867
r_scbond_it3.629
r_mcangle_it3.535
r_mcbond_it2.485
r_angle_refined_deg1.541
r_rigid_bond_restr1.402
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.421
r_dihedral_angle_3_deg10.738
r_dihedral_angle_4_deg10.651
r_dihedral_angle_1_deg6.762
r_scangle_it4.867
r_scbond_it3.629
r_mcangle_it3.535
r_mcbond_it2.485
r_angle_refined_deg1.541
r_rigid_bond_restr1.402
r_angle_other_deg1.39
r_mcbond_other1.092
r_chiral_restr0.109
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1812
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms105

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection