X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4QKN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M sodium citrate (pH 5.8), 12 % (w/v) polyethylene glycol 3350, 8 % isopropanol
Crystal Properties
Matthews coefficientSolvent content
3.0263.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.124α = 90
b = 142.124β = 90
c = 84.539γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2018-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9735SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.353099.70.0570.060.0213.99.826488
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)
12.352.4399.21.1621.2320.4030.7528.8

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 REPLACEMENTTHROUGHOUT4QKN2.353022821125090.790.22280.22070.2643RANDOM37.38
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]
-0.14-0.07-0.140.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.35
r_dihedral_angle_4_deg15.496
r_dihedral_angle_3_deg14.666
r_dihedral_angle_1_deg6.821
r_angle_refined_deg1.318
r_angle_other_deg0.912
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.35
r_dihedral_angle_4_deg15.496
r_dihedral_angle_3_deg14.666
r_dihedral_angle_1_deg6.821
r_angle_refined_deg1.318
r_angle_other_deg0.912
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3361
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing