X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7JRN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52890.1 M MIB buffer pH 6.5, 0.2M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.8155

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.713α = 90
b = 147.365β = 99.72
c = 60.277γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2020-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.1271APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.346.2995.10.1640.1960.1060.98853.333851
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)
12.32.3876.10.1480.52.3

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 REPLACEMENTTHROUGHOUT7JRN2.346.2932102172394.980.21960.21740.2598RANDOM52.873
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]
1.631.020.03-1.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.758
r_dihedral_angle_3_deg16.844
r_dihedral_angle_4_deg16.284
r_dihedral_angle_1_deg6.291
r_angle_refined_deg1.322
r_angle_other_deg1.119
r_chiral_restr0.047
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.758
r_dihedral_angle_3_deg16.844
r_dihedral_angle_4_deg16.284
r_dihedral_angle_1_deg6.291
r_angle_refined_deg1.322
r_angle_other_deg1.119
r_chiral_restr0.047
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5014
Nucleic Acid Atoms
Solvent Atoms33
Heterogen Atoms118

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction