5NLO

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 pH 5.5)
Crystal Properties
Matthews coefficientSolvent content
3.2562.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.35α = 90
b = 125.35β = 90
c = 125.35γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-11-27MSINGLE 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
11.33501000.098120.1321.6677258-3
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)
11.331.361002.620.5161.3721.88

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 REPLACEMENTTHROUGHOUT5ACH1.335073427383199.960.116210.114760.14269RANDOM19.948
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_sphericity_free51.38
r_dihedral_angle_2_deg30.382
r_sphericity_bonded13.739
r_dihedral_angle_4_deg12.551
r_dihedral_angle_3_deg10.075
r_long_range_B_refined7.927
r_long_range_B_other7.926
r_dihedral_angle_1_deg6.112
r_rigid_bond_restr5.34
r_scangle_other3.639
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free51.38
r_dihedral_angle_2_deg30.382
r_sphericity_bonded13.739
r_dihedral_angle_4_deg12.551
r_dihedral_angle_3_deg10.075
r_long_range_B_refined7.927
r_long_range_B_other7.926
r_dihedral_angle_1_deg6.112
r_rigid_bond_restr5.34
r_scangle_other3.639
r_scbond_other3.089
r_scbond_it3.088
r_mcangle_other2.31
r_mcangle_it2.307
r_mcbond_other2.154
r_mcbond_it2.151
r_angle_refined_deg2.028
r_angle_other_deg1.904
r_chiral_restr0.157
r_bond_refined_d0.024
r_gen_planes_other0.015
r_gen_planes_refined0.013
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1788
Nucleic Acid Atoms
Solvent Atoms434
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing