X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529133% PEG 6000 100mM Tris pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.4349.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.937α = 90
b = 36.498β = 116.65
c = 60.7γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FMirrors2016-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.999SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.3654.2595.30.0720.0310.99813.36.245812
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.361.3990.21.1150.510.511.45.4

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 REPLACEMENTTHROUGHOUT3zcf1.3654.2543449236295.330.1460.14430.175RANDOM18.567
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]
0.45-0.370.44-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.119
r_dihedral_angle_4_deg25.496
r_sphericity_free22.279
r_dihedral_angle_3_deg12.7
r_sphericity_bonded7.515
r_dihedral_angle_1_deg6.386
r_angle_other_deg2.604
r_angle_refined_deg2.179
r_rigid_bond_restr2.11
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.119
r_dihedral_angle_4_deg25.496
r_sphericity_free22.279
r_dihedral_angle_3_deg12.7
r_sphericity_bonded7.515
r_dihedral_angle_1_deg6.386
r_angle_other_deg2.604
r_angle_refined_deg2.179
r_rigid_bond_restr2.11
r_chiral_restr0.09
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1628
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing