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
2.856.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.87α = 88.65
b = 76.72β = 64.31
c = 82.8γ = 75.22
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-09-29MSINGLE 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
11.835.290.40.116.13.2130327
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)
11.81.957.60.651.63.1

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 3NXQ1.874.24123869645590.420.20360.202320.22822RANDOM28.59
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]
0.071.720.171.25-0.26-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.683
r_dihedral_angle_4_deg17.242
r_dihedral_angle_3_deg14.387
r_dihedral_angle_1_deg5.72
r_mcangle_it2.17
r_scbond_it1.704
r_angle_refined_deg1.367
r_mcbond_it1.347
r_chiral_restr0.095
r_bond_refined_d0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.683
r_dihedral_angle_4_deg17.242
r_dihedral_angle_3_deg14.387
r_dihedral_angle_1_deg5.72
r_mcangle_it2.17
r_scbond_it1.704
r_angle_refined_deg1.367
r_mcbond_it1.347
r_chiral_restr0.095
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms9892
Nucleic Acid Atoms
Solvent Atoms776
Heterogen Atoms293

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing