5NLN

Auxiliary activity 9


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ACH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52983.6M NaCl 0.1 M citric acid pH4.5 (soaked in pH5.5)
Crystal Properties
Matthews coefficientSolvent content
3.2462.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.3α = 90
b = 125.3β = 90
c = 125.3γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87260ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.95099.80.2890.9886.38.6727034-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9597.71.580.6258.84

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 REPLACEMENTTHROUGHOUT5ACH1.95025655137999.760.166260.163980.20707RANDOM19.634
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.479
r_dihedral_angle_4_deg13.126
r_dihedral_angle_3_deg9.011
r_dihedral_angle_1_deg6.585
r_long_range_B_refined6.199
r_long_range_B_other6.199
r_scangle_other2.81
r_mcangle_other2.123
r_mcangle_it2.121
r_scbond_it1.931
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.479
r_dihedral_angle_4_deg13.126
r_dihedral_angle_3_deg9.011
r_dihedral_angle_1_deg6.585
r_long_range_B_refined6.199
r_long_range_B_other6.199
r_scangle_other2.81
r_mcangle_other2.123
r_mcangle_it2.121
r_scbond_it1.931
r_scbond_other1.931
r_angle_refined_deg1.739
r_mcbond_it1.508
r_mcbond_other1.502
r_angle_other_deg0.996
r_chiral_restr0.113
r_bond_refined_d0.017
r_gen_planes_refined0.011
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 Atoms1788
Nucleic Acid Atoms
Solvent Atoms399
Heterogen Atoms71

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement