X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J6ZPDB ENTRY 1J6Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.6100 MM MES PH 6.6 14% (W/W) PEG1500 12% (W/W) 1,6-HEXANEDIOL 100 MM CACL2 1 MM DTT 10 MM BETAINE-HYDROCHLORIDE
Crystal Properties
Matthews coefficientSolvent content
2.3748.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.653α = 90
b = 194.863β = 90
c = 53.038γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X12EMBL/DESY, HAMBURGX12

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
12.355099.80.0528.489855341
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)
12.352.599.50.553.57.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1J6Z2.3519.413258917601000.1890.1860.241RANDOM46.01
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]
0.210.01-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.748
r_dihedral_angle_4_deg14.892
r_dihedral_angle_3_deg12.024
r_scangle_it3.406
r_dihedral_angle_1_deg3.297
r_mcangle_it3.267
r_scbond_it2.468
r_mcbond_it2.394
r_angle_refined_deg1.709
r_angle_other_deg1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.748
r_dihedral_angle_4_deg14.892
r_dihedral_angle_3_deg12.024
r_scangle_it3.406
r_dihedral_angle_1_deg3.297
r_mcangle_it3.267
r_scbond_it2.468
r_mcbond_it2.394
r_angle_refined_deg1.709
r_angle_other_deg1.03
r_symmetry_vdw_refined0.319
r_xyhbond_nbd_refined0.238
r_symmetry_vdw_other0.228
r_symmetry_hbond_refined0.217
r_nbd_refined0.202
r_nbd_other0.192
r_nbtor_refined0.176
r_chiral_restr0.11
r_nbtor_other0.087
r_bond_refined_d0.017
r_gen_planes_refined0.003
r_bond_other_d0.002
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5383
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms194

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing