X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DDK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.529320% polyethylene glycol (PEG) 550 monomethyl ether (MME), 10% PEG 20 000, 50 mM HEPES, 50 mM MOPS
Crystal Properties
Matthews coefficientSolvent content
1.8132.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.397α = 90
b = 46.977β = 90
c = 183.758γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42009-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.7991.8999.60.08829.612.938481
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)
11.791.8696.60.5012.57

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 REPLACEMENTTHROUGHOUT1DDK1.7991.8836522188799.410.173160.172350.18907RANDOM35.641
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]
-0.610.75-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.256
r_dihedral_angle_3_deg13.088
r_dihedral_angle_4_deg9.296
r_dihedral_angle_1_deg6.248
r_long_range_B_refined4.816
r_long_range_B_other4.538
r_angle_refined_deg1.229
r_mcangle_it1.15
r_mcangle_other1.15
r_scangle_other1.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.256
r_dihedral_angle_3_deg13.088
r_dihedral_angle_4_deg9.296
r_dihedral_angle_1_deg6.248
r_long_range_B_refined4.816
r_long_range_B_other4.538
r_angle_refined_deg1.229
r_mcangle_it1.15
r_mcangle_other1.15
r_scangle_other1.011
r_angle_other_deg0.895
r_mcbond_it0.661
r_mcbond_other0.658
r_scbond_it0.576
r_scbond_other0.575
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3434
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing