X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HNH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.32790.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties
Matthews coefficientSolvent content
2.2344.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.017α = 90
b = 56.98β = 93.78
c = 135.073γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rbeamline optics2012-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95369Australian SynchrotronMX2

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
12.155097.20.09510.413.16725767257-1-1
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)
12.152.190.4991.92.93361

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2HNH2.1535.286712667126338496.910.229480.229480.22620.29079RANDOM22.248
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]
2.451.090.63-2.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.85
r_dihedral_angle_4_deg22.254
r_dihedral_angle_3_deg17.169
r_scangle_it7.272
r_dihedral_angle_1_deg6.613
r_scbond_it5.553
r_mcangle_it3.475
r_mcbond_it2.504
r_angle_refined_deg1.745
r_chiral_restr0.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.85
r_dihedral_angle_4_deg22.254
r_dihedral_angle_3_deg17.169
r_scangle_it7.272
r_dihedral_angle_1_deg6.613
r_scbond_it5.553
r_mcangle_it3.475
r_mcbond_it2.504
r_angle_refined_deg1.745
r_chiral_restr0.119
r_bond_refined_d0.019
r_gen_planes_refined0.009
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9700
Nucleic Acid Atoms
Solvent Atoms277
Heterogen Atoms

Software

Software
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing