X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5291Tris/Acetate 0.1M, MgCl2 0.2M, PEG 3350 27%
Crystal Properties
Matthews coefficientSolvent content
2.0239.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.697α = 82.67
b = 48.315β = 86.76
c = 71.942γ = 69.95
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2015-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

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
11.5145.0895.90.0840.0980.0490.99812.146957710.3
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)
11.511.5374.90.830.9660.4920.5933.7

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 REPLACEMENTTHROUGHOUT4DNP1.5136.2766090348595.870.16610.16440.1973RANDOM19.047
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]
-0.10.12-0.09-0.010.20.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.059
r_dihedral_angle_4_deg15.842
r_dihedral_angle_3_deg13.102
r_dihedral_angle_1_deg5.677
r_angle_refined_deg1.76
r_angle_other_deg1.436
r_chiral_restr0.112
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_gen_planes_other0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.059
r_dihedral_angle_4_deg15.842
r_dihedral_angle_3_deg13.102
r_dihedral_angle_1_deg5.677
r_angle_refined_deg1.76
r_angle_other_deg1.436
r_chiral_restr0.112
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_gen_planes_other0.01
r_bond_other_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4154
Nucleic Acid Atoms
Solvent Atoms450
Heterogen Atoms46

Software

Software
Software NamePurpose
XDSdata scaling
Aimlessdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction