X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7.52910.2M NaF 20% PEG3350 Fe-Azotochelin stock solution
Crystal Properties
Matthews coefficientSolvent content
2.550.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.139α = 82.71
b = 63.41β = 76.36
c = 67.674γ = 79.03
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.865.5299.10.0550.99813.31.884430
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)
11.81.8397.90.390.58915.3

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 REPLACEMENTTHROUGHOUT3zkw1.865.5284411431499.090.2070.20470.251RANDOM39.161
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]
-2.05-1.050.91-0.292.392.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.792
r_dihedral_angle_3_deg16.339
r_dihedral_angle_4_deg15.347
r_dihedral_angle_1_deg6.613
r_mcangle_it4.62
r_angle_other_deg3.769
r_mcbond_it3.493
r_mcbond_other3.493
r_angle_refined_deg1.959
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.792
r_dihedral_angle_3_deg16.339
r_dihedral_angle_4_deg15.347
r_dihedral_angle_1_deg6.613
r_mcangle_it4.62
r_angle_other_deg3.769
r_mcbond_it3.493
r_mcbond_other3.493
r_angle_refined_deg1.959
r_chiral_restr0.122
r_gen_planes_other0.024
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6729
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing