X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82980.1M PCB buffer, pH 8, 25% PEG 1500 +cryo 33% PEG 1500 in well solution
Crystal Properties
Matthews coefficientSolvent content
2.5351.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.696α = 82.09
b = 62.881β = 74.67
c = 69.867γ = 77.6
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2016-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979DiamondI02

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
11.967.1395.90.1020.9916.23.470811
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)
11.91.94960.9560.4181.33.5

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 REPLACEMENTTHROUGHOUT3ZKW1.967.1367360345195.850.173550.171430.21499RANDOM34.815
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]
0.76-0.790.14-0.751.23-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.078
r_dihedral_angle_3_deg15.013
r_dihedral_angle_4_deg11.591
r_long_range_B_other7.33
r_long_range_B_refined7.326
r_dihedral_angle_1_deg6.319
r_scangle_other6.277
r_scbond_it4.149
r_scbond_other4.148
r_mcangle_it3.798
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.078
r_dihedral_angle_3_deg15.013
r_dihedral_angle_4_deg11.591
r_long_range_B_other7.33
r_long_range_B_refined7.326
r_dihedral_angle_1_deg6.319
r_scangle_other6.277
r_scbond_it4.149
r_scbond_other4.148
r_mcangle_it3.798
r_mcangle_other3.798
r_mcbond_it2.858
r_mcbond_other2.858
r_angle_refined_deg1.85
r_angle_other_deg1.041
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6586
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing