X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DM6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529916% PEG8000, 0.1M citrate, 0.3M lithium sulphate, 0.1M sodium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K
Crystal Properties
Matthews coefficientSolvent content
3.0459.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.838α = 90
b = 103.075β = 103.32
c = 100.499γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IV2006-09-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
12.597.5999.75331738.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.56100

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 REPLACEMENTTHROUGHOUT3DM62.540.2653317284999.70.2320.2290.282RANDOM38.2
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]
-0.13-0.170.37-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.703
r_dihedral_angle_4_deg18.528
r_dihedral_angle_3_deg16.896
r_dihedral_angle_1_deg8.076
r_scangle_it5.697
r_scbond_it4.002
r_mcangle_it2.709
r_angle_refined_deg1.992
r_mcbond_it1.672
r_nbtor_refined0.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.703
r_dihedral_angle_4_deg18.528
r_dihedral_angle_3_deg16.896
r_dihedral_angle_1_deg8.076
r_scangle_it5.697
r_scbond_it4.002
r_mcangle_it2.709
r_angle_refined_deg1.992
r_mcbond_it1.672
r_nbtor_refined0.335
r_symmetry_vdw_refined0.281
r_nbd_refined0.233
r_chiral_restr0.146
r_xyhbond_nbd_refined0.141
r_symmetry_hbond_refined0.04
r_bond_refined_d0.016
r_gen_planes_refined0.008
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 Atoms8805
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms180

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling