X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZKMPDB code 2ZKM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7277.15100 mM Bis-Tris, 100 mM NaCl, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
2.3948.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.815α = 90
b = 89.396β = 90
c = 163.051γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDRayonix MarMosiac 225tiled fiber-optic tapers2009-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.979APS21-ID-F

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
11.895097.70.0697.43.77006370063-999999-2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.9297.53.1

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB code 2ZKM227.367006353335282692.30.177540.175890.20819RANDOM30.916
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.128
r_dihedral_angle_4_deg14.032
r_dihedral_angle_3_deg11.666
r_dihedral_angle_1_deg5.422
r_scangle_it1.892
r_scbond_it1.144
r_angle_refined_deg0.946
r_angle_other_deg0.743
r_mcangle_it0.732
r_mcbond_it0.373
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.128
r_dihedral_angle_4_deg14.032
r_dihedral_angle_3_deg11.666
r_dihedral_angle_1_deg5.422
r_scangle_it1.892
r_scbond_it1.144
r_angle_refined_deg0.946
r_angle_other_deg0.743
r_mcangle_it0.732
r_mcbond_it0.373
r_mcbond_other0.065
r_chiral_restr0.057
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6275
Nucleic Acid Atoms
Solvent Atoms452
Heterogen Atoms55

Software

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