X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JALPDB Entries 1JAL and 1NI3
experimental modelPDB 1NI3PDB Entries 1JAL and 1NI3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP827712% PEG 3350, 50 mM TRIS/HCl, 10 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.4764.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.253α = 90
b = 159.831β = 90
c = 55.129γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMirrors2005-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.9764SLSX06SA

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
12.75099.80.08416.37.21759017590-370.7
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)
12.72.81000.822.87.41797

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 REPLACEMENTTHROUGHOUTPDB Entries 1JAL and 1NI32.750175891758989199.80.2330.2330.230.288RANDOM50.599
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]
-2.152.81-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.263
r_dihedral_angle_3_deg16.622
r_dihedral_angle_4_deg14.939
r_dihedral_angle_1_deg7.013
r_scangle_it6.21
r_scbond_it4.612
r_mcangle_it2.994
r_mcbond_it2.256
r_angle_refined_deg1.438
r_angle_other_deg0.843
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.263
r_dihedral_angle_3_deg16.622
r_dihedral_angle_4_deg14.939
r_dihedral_angle_1_deg7.013
r_scangle_it6.21
r_scbond_it4.612
r_mcangle_it2.994
r_mcbond_it2.256
r_angle_refined_deg1.438
r_angle_other_deg0.843
r_mcbond_other0.462
r_nbd_refined0.239
r_symmetry_vdw_other0.234
r_symmetry_vdw_refined0.202
r_nbtor_refined0.195
r_nbd_other0.182
r_xyhbond_nbd_refined0.151
r_symmetry_hbond_refined0.103
r_nbtor_other0.09
r_chiral_restr0.075
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms2639
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms31

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling