X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZNTPDB ENTRY 2ZNT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.530335% PEG3350, 0.3M LiSO4, 5mM neodysiherbaine A, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties
Matthews coefficientSolvent content
2.2846.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.579α = 85.72
b = 50.712β = 95.79
c = 63.144γ = 62.08
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDRIGAKU JUPITER 2102008-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B10.9SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.55096.90.04232.23.87926779267
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.5595.10.1576.23.87731

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 2ZNT1.53075263399996.730.17140.170160.19456RANDOM9.024
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]
-0.230.22-0.04-0.32-0.010.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.4
r_dihedral_angle_3_deg12.649
r_dihedral_angle_4_deg11.196
r_dihedral_angle_1_deg5.692
r_scangle_it2.558
r_scbond_it1.74
r_angle_refined_deg1.251
r_mcangle_it1.052
r_mcbond_it0.737
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.4
r_dihedral_angle_3_deg12.649
r_dihedral_angle_4_deg11.196
r_dihedral_angle_1_deg5.692
r_scangle_it2.558
r_scbond_it1.74
r_angle_refined_deg1.251
r_mcangle_it1.052
r_mcbond_it0.737
r_nbtor_refined0.307
r_nbd_refined0.193
r_symmetry_vdw_refined0.172
r_symmetry_hbond_refined0.119
r_xyhbond_nbd_refined0.112
r_chiral_restr0.087
r_bond_refined_d0.008
r_gen_planes_refined0.005
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 Atoms4133
Nucleic Acid Atoms
Solvent Atoms471
Heterogen Atoms115

Software

Software
Software NamePurpose
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing