X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PZ3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52932:1 protein:well solution. 0.1 M pH 7.5 Tris-HCl buffer, 18% PEG3350, 0.7 M NH4F, 5% 2-propanol
Crystal Properties
Matthews coefficientSolvent content
2.7354.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.994α = 90
b = 178.994β = 90
c = 100.893γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2018-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.987DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.429.8599.50.0770.99710.86.2235421
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4494.50.6130.781.55.8

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1PZ31.40229.852354201242599.5120.1710.17020.178419.467
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]
0.0550.0270.055-0.177
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.913
r_dihedral_angle_4_deg19.719
r_dihedral_angle_3_deg11.714
r_dihedral_angle_1_deg7.527
r_lrange_it5.435
r_lrange_other5.261
r_scangle_it4.808
r_scangle_other4.808
r_scbond_it3.771
r_scbond_other3.771
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.913
r_dihedral_angle_4_deg19.719
r_dihedral_angle_3_deg11.714
r_dihedral_angle_1_deg7.527
r_lrange_it5.435
r_lrange_other5.261
r_scangle_it4.808
r_scangle_other4.808
r_scbond_it3.771
r_scbond_other3.771
r_mcangle_other2.999
r_mcangle_it2.997
r_angle_other_deg2.537
r_mcbond_it2.464
r_mcbond_other2.463
r_angle_refined_deg2.169
r_symmetry_nbd_refined0.344
r_nbd_other0.318
r_nbd_refined0.226
r_symmetry_nbd_other0.215
r_symmetry_xyhbond_nbd_refined0.194
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.15
r_symmetry_xyhbond_nbd_other0.145
r_chiral_restr0.128
r_symmetry_nbtor_other0.078
r_bond_other_d0.035
r_gen_planes_other0.026
r_bond_refined_d0.019
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7747
Nucleic Acid Atoms
Solvent Atoms859
Heterogen Atoms110

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing