X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6277Protein solution (2mcl): 10.8 mg/mL Tsprol and 150 mM NaCl in 50 mM Tris buffer (pH 7.6). Reservoir solution (2mcl): 100 mM CdCl2 and 30 % v/v PEG400 in 100 mM sodium acetate buffer (pH 4.6), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.968.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.7α = 90
b = 89.7β = 90
c = 165.22γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2010-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONKURCHATOV SNC BEAMLINE K4.40.9887KURCHATOV SNCK4.4

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
12.678.8399.20.08924.52148021360
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)
12.62.899.80.7284.2

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 REPLACEMENTTHROUGHOUT2HOW2.678.8320268109299.440.232930.2310.26859RANDOM49.071
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]
0.570.57-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.07
r_dihedral_angle_3_deg19.525
r_dihedral_angle_4_deg19.166
r_dihedral_angle_1_deg6.142
r_scangle_it2.91
r_scbond_it1.799
r_angle_refined_deg1.384
r_mcangle_it1.276
r_mcbond_it0.683
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.07
r_dihedral_angle_3_deg19.525
r_dihedral_angle_4_deg19.166
r_dihedral_angle_1_deg6.142
r_scangle_it2.91
r_scbond_it1.799
r_angle_refined_deg1.384
r_mcangle_it1.276
r_mcbond_it0.683
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.005
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 Atoms2851
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms12

Software

Software
Software NamePurpose
AUTOMARdata collection
BALBESphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling