X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IAGpdb entry 2iag

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.529120% PEG400, 0.1M potassium chloride, 0.1M trisodium citrate, pH 5.5, vapor diffusion, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
358.3
358.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.339α = 64.36
b = 80.159β = 75.23
c = 84.937γ = 72.17
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 3152007-09-21MSINGLE WAVELENGTH
21x-rayMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X250.96860NSLSX25
2

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
1,22.140920.06311.13.765596
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)
2.12.1868.20.4023.14818

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 DIFFRACTIONmr, MRTHROUGHOUTpdb entry 2iag2.153063038201893.4490.190.1890.228thin shells (sftools)31.625
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]
-0.061-0.162-0.0070.0810.19-0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.131
r_dihedral_angle_4_deg18.185
r_dihedral_angle_3_deg14.595
r_dihedral_angle_1_deg5.969
r_mcangle_it3.606
r_scangle_it3.393
r_mcbond_it2.526
r_scbond_it2.432
r_angle_refined_deg1.288
r_angle_other_deg0.877
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.131
r_dihedral_angle_4_deg18.185
r_dihedral_angle_3_deg14.595
r_dihedral_angle_1_deg5.969
r_mcangle_it3.606
r_scangle_it3.393
r_mcbond_it2.526
r_scbond_it2.432
r_angle_refined_deg1.288
r_angle_other_deg0.877
r_mcbond_other0.615
r_symmetry_hbond_refined0.217
r_symmetry_vdw_other0.205
r_nbd_refined0.202
r_nbd_other0.188
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.122
r_symmetry_vdw_refined0.098
r_nbtor_other0.086
r_chiral_restr0.079
r_bond_refined_d0.017
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7519
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms88

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
MolProbitymodel building