X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52984.4 M NaCl 0.1 M citric acid, pH4.5 (soaked in pH 5.5)
Crystal Properties
Matthews coefficientSolvent content
3.2361.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.17α = 90
b = 125.17β = 90
c = 125.17γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97625ESRFID23-1

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
11.55099.70.1140.99816.8410.4153847-3
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)
11.51.5499.91.670.5169.64

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 REPLACEMENTTHROUGHOUT5ACH1.55051121272699.70.139360.137570.17179RANDOM19.968
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_deg34.44
r_sphericity_bonded13.153
r_dihedral_angle_4_deg11.96
r_dihedral_angle_3_deg10.05
r_rigid_bond_restr8.496
r_dihedral_angle_1_deg7.563
r_long_range_B_other5.782
r_long_range_B_refined5.781
r_scangle_other5.277
r_scbond_it4.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.44
r_sphericity_bonded13.153
r_dihedral_angle_4_deg11.96
r_dihedral_angle_3_deg10.05
r_rigid_bond_restr8.496
r_dihedral_angle_1_deg7.563
r_long_range_B_other5.782
r_long_range_B_refined5.781
r_scangle_other5.277
r_scbond_it4.306
r_scbond_other4.306
r_mcangle_other3.387
r_mcangle_it3.365
r_mcbond_it3.169
r_mcbond_other3.16
r_angle_refined_deg1.898
r_angle_other_deg0.905
r_chiral_restr0.128
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
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_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1788
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing