X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NTY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.328923-27% (w/v) PEG 4000, 100 mM Hepes, 10mM CaCl2, 0.4M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.346.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.545α = 90
b = 76.168β = 94.88
c = 88.706γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDOXFORD ONYX CCDOXFORD ONYX CCD2014-08-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION ENHANCE ULTRA1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.688.38599.810.2770.145.13.92032719305
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6671000.6670.6670.3950.93.92923

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 REPLACEMENTTHROUGHOUT3NTY2.688.3819305100699.810.213380.211590.24724RANDOM19.05
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]
-1.04-0.66-0.81.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.116
r_dihedral_angle_4_deg15.468
r_dihedral_angle_3_deg13.958
r_dihedral_angle_1_deg6.63
r_long_range_B_refined3.601
r_long_range_B_other3.569
r_scangle_other1.944
r_mcangle_it1.853
r_mcangle_other1.853
r_angle_refined_deg1.571
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.116
r_dihedral_angle_4_deg15.468
r_dihedral_angle_3_deg13.958
r_dihedral_angle_1_deg6.63
r_long_range_B_refined3.601
r_long_range_B_other3.569
r_scangle_other1.944
r_mcangle_it1.853
r_mcangle_other1.853
r_angle_refined_deg1.571
r_scbond_it1.118
r_scbond_other1.118
r_mcbond_it1.069
r_mcbond_other1.069
r_angle_other_deg1
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5092
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms162

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction