X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NT0PDB entry 2NT0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.52980.8 M Na H2PO4, 0.8 M K H2PO4, 0.1 M Citrate pH 5.5 soaked with acetate buffer pH 4.5 and 1.8 M Li2SO4 prior to freezing, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.2161.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.442α = 90
b = 91.703β = 111.04
c = 152.491γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.514281268
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.562.1

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 DIFFRACTIONTHROUGHOUTPDB entry 2NT02.542.1481268434287.660.2080.2040.275RANDOM49.621
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]
0.080.06-0.140.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.923
r_dihedral_angle_4_deg23.621
r_dihedral_angle_3_deg19.519
r_dihedral_angle_1_deg7.851
r_scangle_it3.501
r_scbond_it2.223
r_angle_refined_deg1.873
r_mcangle_it1.668
r_mcbond_it0.955
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.923
r_dihedral_angle_4_deg23.621
r_dihedral_angle_3_deg19.519
r_dihedral_angle_1_deg7.851
r_scangle_it3.501
r_scbond_it2.223
r_angle_refined_deg1.873
r_mcangle_it1.668
r_mcbond_it0.955
r_nbtor_refined0.322
r_symmetry_vdw_refined0.269
r_nbd_refined0.241
r_xyhbond_nbd_refined0.184
r_symmetry_hbond_refined0.16
r_chiral_restr0.128
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15720
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms334

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
REFMACphasing