X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NXQPDB ENTRY 3NXQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.06 M DIVALENT CATIONS, 0.1 M TRIS/BICINE PH 8.5, 30 % PEG550MME/PEG20000
Crystal Properties
Matthews coefficientSolvent content
358

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.48α = 85.46
b = 101.59β = 85.9
c = 114.51γ = 81.62
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.830.397.20.16.23.2293868
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)
11.81.9960.71.53.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3NXQ1.8113.942792711457797.240.208120.206710.2351RANDOM29.206
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]
-0.92-0.47-0.080.30.140.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.871
r_dihedral_angle_4_deg17.054
r_dihedral_angle_3_deg13.37
r_dihedral_angle_1_deg5.273
r_mcangle_it1.497
r_scbond_it1.24
r_angle_refined_deg1.185
r_mcbond_it0.878
r_chiral_restr0.084
r_bond_refined_d0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.871
r_dihedral_angle_4_deg17.054
r_dihedral_angle_3_deg13.37
r_dihedral_angle_1_deg5.273
r_mcangle_it1.497
r_scbond_it1.24
r_angle_refined_deg1.185
r_mcbond_it0.878
r_chiral_restr0.084
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19752
Nucleic Acid Atoms
Solvent Atoms1611
Heterogen Atoms644

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing