X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HCK1hck, 2b9r, 1jst
experimental modelPDB 2B9R1hck, 2b9r, 1jst
experimental modelPDB 1JST1hck, 2b9r, 1jst

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.7277Conditions around 0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml
Crystal Properties
Matthews coefficientSolvent content
2.4549.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.166α = 90
b = 68.646β = 90
c = 166.771γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97957DiamondI02

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
12.35399.90.08613.76.73408534085
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)
12.32.3899.90.7782.46.4

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 REPLACEMENTTHROUGHOUT1hck, 2b9r, 1jst2.35334010169799.820.18950.18610.2519RANDOM48.7092
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]
-0.41-0.681.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.587
r_dihedral_angle_4_deg16.486
r_dihedral_angle_3_deg16.044
r_dihedral_angle_1_deg6.567
r_angle_other_deg3.568
r_mcangle_it2.273
r_angle_refined_deg1.568
r_mcbond_it1.279
r_mcbond_other1.279
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.587
r_dihedral_angle_4_deg16.486
r_dihedral_angle_3_deg16.044
r_dihedral_angle_1_deg6.567
r_angle_other_deg3.568
r_mcangle_it2.273
r_angle_refined_deg1.568
r_mcbond_it1.279
r_mcbond_other1.279
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_other0.008
r_gen_planes_refined0.007
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5139
Nucleic Acid Atoms
Solvent Atoms368
Heterogen Atoms26

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement