X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QSD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293Reservoir: 0.1M Ammonium Acetate, 0.1M Bis-Tris, 17% PEG 10000. Protein buffer and concentration: 5mM Sodium Acetate, pH 5.5, Cpr=5.25mg/ml. Ratio Protein: Reservoir=2:1. Cryocooled in mother liquor containing 20% ethylene glycol., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.448.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.281α = 76.97
b = 83.172β = 86.6
c = 84.569γ = 71.11
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDDouble crystal monochromator with 2 sets of Rh-soated silicon and glass mirrors2011-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.914BESSY14.2

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
11.955078.40.03725.92.37865025.2
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)
11.951.9842.10.2963.11.9

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 REPLACEMENTTHROUGHOUT3QSD1.9538.49514271614375675.270.201950.201950.199270.25245RANDOM21.792
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]
0.010.010.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.195
r_dihedral_angle_4_deg17.278
r_dihedral_angle_3_deg15.521
r_dihedral_angle_1_deg6.062
r_scangle_it2.26
r_scbond_it1.513
r_angle_refined_deg1.303
r_mcangle_it0.911
r_mcbond_it0.565
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.195
r_dihedral_angle_4_deg17.278
r_dihedral_angle_3_deg15.521
r_dihedral_angle_1_deg6.062
r_scangle_it2.26
r_scbond_it1.513
r_angle_refined_deg1.303
r_mcangle_it0.911
r_mcbond_it0.565
r_nbtor_refined0.306
r_symmetry_hbond_refined0.227
r_nbd_refined0.205
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.151
r_chiral_restr0.098
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9797
Nucleic Acid Atoms
Solvent Atoms519
Heterogen Atoms24

Software

Software
Software NamePurpose
MarDBdata collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling