X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ZDC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72921 M sodium succinate pH 7.0, 1% w/v PEG-MME2000 Protein at 10 mg/ml in buffer: 25 mM HEPES pH 7.0, 200 mM NaCl 100 nl protein solution and 200 nl reservoir solution.
Crystal Properties
Matthews coefficientSolvent content
2.7154.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.245α = 90
b = 144.245β = 90
c = 139.661γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
13102.2051000.5820.6110.1350.974520.33016141.75
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.1699.81.1751.2050.2650.2532.920.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6ZDC3102.20530099142999.9470.2180.21530.2687RANDOM49.027
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]
0.310.31-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.265
r_dihedral_angle_3_deg19.232
r_dihedral_angle_4_deg17.66
r_lrange_it7.502
r_dihedral_angle_1_deg5.968
r_scangle_it4.687
r_mcangle_it4.566
r_scbond_it2.899
r_mcbond_it2.769
r_angle_refined_deg1.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.265
r_dihedral_angle_3_deg19.232
r_dihedral_angle_4_deg17.66
r_lrange_it7.502
r_dihedral_angle_1_deg5.968
r_scangle_it4.687
r_mcangle_it4.566
r_scbond_it2.899
r_mcbond_it2.769
r_angle_refined_deg1.7
r_nbtor_refined0.298
r_symmetry_xyhbond_nbd_refined0.249
r_symmetry_nbd_refined0.205
r_nbd_refined0.18
r_chiral_restr0.126
r_xyhbond_nbd_refined0.11
r_ncsr_local_group_20.085
r_ncsr_local_group_10.082
r_ncsr_local_group_30.074
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8853
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing