X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YD9PDB ENTRIES 1YD9, 1ZR3, 1ZR5, 3IID
experimental modelPDB 1ZR3PDB ENTRIES 1YD9, 1ZR3, 1ZR5, 3IID
experimental modelPDB 1ZR5PDB ENTRIES 1YD9, 1ZR3, 1ZR5, 3IID
experimental modelPDB 3IIDPDB ENTRIES 1YD9, 1ZR3, 1ZR5, 3IID

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.05M MGCL2; 0.1M HEPES PH 7.5; 30% MPEG 550
Crystal Properties
Matthews coefficientSolvent content
1.7529.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.03α = 90
b = 61.64β = 89.64
c = 242.23γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
12.141.8692.70.077.52.445536232.2
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)
12.12.2177.70.372.32.3

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 ENTRIES 1YD9, 1ZR3, 1ZR5, 3IID2.094043253228190.550.219220.217430.25298RANDOM33.822
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]
1.930.32-10.959.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.208
r_dihedral_angle_3_deg17.054
r_dihedral_angle_4_deg12.436
r_dihedral_angle_1_deg6.203
r_angle_refined_deg1.45
r_angle_other_deg1.314
r_chiral_restr0.087
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.208
r_dihedral_angle_3_deg17.054
r_dihedral_angle_4_deg12.436
r_dihedral_angle_1_deg6.203
r_angle_refined_deg1.45
r_angle_other_deg1.314
r_chiral_restr0.087
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5584
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing