X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FD6PDB ENTRY 2fd6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS7.52958% PEG 4000, 2.5% ethanol, 0.05% sodium azide, 50mM cacodylate pH 6.5, pH 7.5, MICRODIALYSIS, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.8857.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.096α = 90
b = 87.205β = 94.31
c = 124.274γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 210MSINGLE WAVELENGTH
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C1.0APS24-ID-C
2SYNCHROTRONNSLS BEAMLINE X12C1.0NSLSX12C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
1,22.55099.20.0770.07724.15.33838142.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,22.52.59960.3560.3562.84.13675

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 2fd62.542.8837032119199.160.229930.228620.2717RANDOM62.232
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]
-0.13-0.71.5-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.001
r_dihedral_angle_4_deg19.28
r_dihedral_angle_3_deg18.315
r_dihedral_angle_1_deg7.848
r_scangle_it2.926
r_scbond_it2.001
r_angle_refined_deg1.74
r_mcangle_it1.264
r_angle_other_deg1.11
r_mcbond_it1.039
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.001
r_dihedral_angle_4_deg19.28
r_dihedral_angle_3_deg18.315
r_dihedral_angle_1_deg7.848
r_scangle_it2.926
r_scbond_it2.001
r_angle_refined_deg1.74
r_mcangle_it1.264
r_angle_other_deg1.11
r_mcbond_it1.039
r_xyhbond_nbd_other0.417
r_xyhbond_nbd_refined0.236
r_nbd_refined0.227
r_nbd_other0.213
r_symmetry_vdw_other0.184
r_nbtor_refined0.182
r_mcbond_other0.166
r_symmetry_vdw_refined0.135
r_chiral_restr0.122
r_symmetry_hbond_refined0.121
r_nbtor_other0.096
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms6527
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing