X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5293.1517 % (w/v) PEG MME 5000, 0.1 M sodium acetate, pH 5.5, 0.16 M magnesium formate, 20 mM cystamine, protein concentration 8 mg/ml
Crystal Properties
Matthews coefficientSolvent content
2.3748.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.654α = 90
b = 116.774β = 90.797
c = 109.903γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.0332PETRA III, EMBL c/o DESYP13 (MX1)

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
11.3146.6995.40.0450.0530.0290.99911.23.2268173-3.712.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.311.3396.80.4890.5990.340.79522.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4YNT1.3146.69268125534695.3480.1070.10720.10590.137random selection17.369
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]
0.5680.2930.335-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.992
r_dihedral_angle_4_deg18.812
r_dihedral_angle_3_deg11.281
r_dihedral_angle_1_deg6.958
r_rigid_bond_restr3.354
r_lrange_it3.215
r_scangle_it2.907
r_scangle_other2.907
r_lrange_other2.871
r_scbond_it2.541
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.992
r_dihedral_angle_4_deg18.812
r_dihedral_angle_3_deg11.281
r_dihedral_angle_1_deg6.958
r_rigid_bond_restr3.354
r_lrange_it3.215
r_scangle_it2.907
r_scangle_other2.907
r_lrange_other2.871
r_scbond_it2.541
r_scbond_other2.541
r_mcangle_other2.009
r_mcangle_it2.007
r_angle_refined_deg1.825
r_mcbond_it1.655
r_mcbond_other1.655
r_angle_other_deg1.572
r_nbd_refined0.219
r_nbd_other0.211
r_symmetry_xyhbond_nbd_refined0.192
r_symmetry_nbd_other0.191
r_symmetry_nbd_refined0.179
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.138
r_chiral_restr0.109
r_symmetry_nbtor_other0.085
r_symmetry_xyhbond_nbd_other0.061
r_bond_refined_d0.013
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8922
Nucleic Acid Atoms
Solvent Atoms1664
Heterogen Atoms267

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MoRDaphasing