X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VKKPDB ENTRY 1VKK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52772.0M NaCl, 10% PEG 6000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1943.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.87α = 90
b = 78.15β = 90
c = 57.3γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9796DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.946.2199.80.1220.1229.5522857
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.921000.8650.8651.95.116823

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1VKK1.946.212168521685117299.660.192710.192710.189410.25493RANDOM12.504
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]
-0.33-0.470.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.391
r_dihedral_angle_4_deg16.422
r_dihedral_angle_3_deg14.62
r_scangle_it9.388
r_scbond_it8.201
r_dihedral_angle_1_deg6.311
r_mcangle_it5.681
r_mcbond_it4.53
r_mcbond_other1.948
r_angle_refined_deg1.448
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.391
r_dihedral_angle_4_deg16.422
r_dihedral_angle_3_deg14.62
r_scangle_it9.388
r_scbond_it8.201
r_dihedral_angle_1_deg6.311
r_mcangle_it5.681
r_mcbond_it4.53
r_mcbond_other1.948
r_angle_refined_deg1.448
r_angle_other_deg0.859
r_chiral_restr0.084
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2217
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms2

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling