X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QFKPDB ENTRY 2QFK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.92770.2 M AMMONIUM SULFATE, 32% PEG 4000, PH 5.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Crystal Properties
Matthews coefficientSolvent content
2.1843.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.007α = 90
b = 67.358β = 90
c = 69.42γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2007-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.91942APS22-ID

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
11.063598.70.05222.5412197011585426.8
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)
1.061.0993.80.3183.83.38490

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 ENTRY 2QFK1.06352121970115854611698.70.1690.1680.183RANDOM10.17
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]
0.02-0.10.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.01
r_dihedral_angle_4_deg15.961
r_dihedral_angle_3_deg14.42
r_dihedral_angle_1_deg3.973
r_sphericity_free2.377
r_scangle_it1.898
r_sphericity_bonded1.618
r_scbond_it1.352
r_angle_refined_deg1.17
r_mcangle_it1.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.01
r_dihedral_angle_4_deg15.961
r_dihedral_angle_3_deg14.42
r_dihedral_angle_1_deg3.973
r_sphericity_free2.377
r_scangle_it1.898
r_sphericity_bonded1.618
r_scbond_it1.352
r_angle_refined_deg1.17
r_mcangle_it1.074
r_rigid_bond_restr0.74
r_mcbond_it0.663
r_nbtor_refined0.308
r_nbd_refined0.21
r_symmetry_vdw_refined0.178
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.12
r_chiral_restr0.088
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2182
Nucleic Acid Atoms
Solvent Atoms356
Heterogen Atoms112

Software

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