X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D1I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291Sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.6854.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.12α = 90.2
b = 115.91β = 89.96
c = 116.103γ = 90.08
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.46116.196.40.9969.63.4865389
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.461.480.662

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 REPLACEMENTTHROUGHOUT4D1I1.46116.18219334336996.350.12820.12590.1718RANDOM22.723
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]
0.310.63-0.4-1.36-0.611.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.449
r_dihedral_angle_4_deg20.005
r_dihedral_angle_3_deg11.998
r_dihedral_angle_1_deg7.25
r_rigid_bond_restr5.156
r_angle_refined_deg1.979
r_angle_other_deg1.608
r_chiral_restr0.115
r_bond_refined_d0.017
r_gen_planes_refined0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.449
r_dihedral_angle_4_deg20.005
r_dihedral_angle_3_deg11.998
r_dihedral_angle_1_deg7.25
r_rigid_bond_restr5.156
r_angle_refined_deg1.979
r_angle_other_deg1.608
r_chiral_restr0.115
r_bond_refined_d0.017
r_gen_planes_refined0.014
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms33818
Nucleic Acid Atoms
Solvent Atoms5125
Heterogen Atoms256

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
REFMACphasing