X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DT3PDB ENTRY 1DT3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.550 % PEG400, 0.2 M LITHIUM SULFATE, 0.1 M NA-ACETATE PH 4.5, SITTING DROP, VAPOUR DIFFUSION
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.478α = 90
b = 90.478β = 90
c = 160.455γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1102015-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.850.0299.90.0720.913.1593912
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)
11.81.8497.70.87312.8

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 ENTRY 1DT31.850.0259391306199.840.172720.171520.19693RANDOM36.267
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]
0.40.4-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.36
r_dihedral_angle_4_deg15.232
r_dihedral_angle_3_deg12.325
r_dihedral_angle_1_deg6.256
r_mcangle_it1.769
r_angle_refined_deg1.706
r_scbond_it1.65
r_angle_other_deg1.497
r_mcbond_it1.125
r_mcbond_other1.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.36
r_dihedral_angle_4_deg15.232
r_dihedral_angle_3_deg12.325
r_dihedral_angle_1_deg6.256
r_mcangle_it1.769
r_angle_refined_deg1.706
r_scbond_it1.65
r_angle_other_deg1.497
r_mcbond_it1.125
r_mcbond_other1.125
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.008
r_gen_planes_other0.007
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_mcangle_other
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 Atoms4061
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing