X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NCI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7289.150.7M Sodium citrate tribasic dihydrate, 0.1M Bis-Tris propane (pH 7.0)
Crystal Properties
Matthews coefficientSolvent content
3.3963.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.6α = 90
b = 106.6β = 90
c = 143.7γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.979SSRFBL17U1

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
11.885099.70.13325.315.264234
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.9399.80.9515.48

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 REPLACEMENTTHROUGHOUT5NCI1.8842.7864234338199.720.13590.13340.1836RANDOM29.333
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]
0.220.22-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.384
r_dihedral_angle_2_deg11.294
r_dihedral_angle_1_deg6.446
r_rigid_bond_restr4.795
r_angle_refined_deg0.953
r_angle_other_deg0.344
r_chiral_restr0.052
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.384
r_dihedral_angle_2_deg11.294
r_dihedral_angle_1_deg6.446
r_rigid_bond_restr4.795
r_angle_refined_deg0.953
r_angle_other_deg0.344
r_chiral_restr0.052
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4162
Nucleic Acid Atoms
Solvent Atoms576
Heterogen Atoms2

Software

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