X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.52983.2 M NaCl 0.1 M citric acid, pH3.5 (soaked in pH 5.5)
Crystal Properties
Matthews coefficientSolvent content
3.3262.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.3α = 90
b = 126.3β = 90
c = 126.3γ = 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
11.755099.10.1180.99711.5310.3634937-3
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)
11.751.898.41.810.4041.0210.07

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 REPLACEMENTTHROUGHOUT5ACH1.755033115178398.940.183230.181480.21445RANDOM32.736
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_deg31.6
r_dihedral_angle_4_deg15.847
r_dihedral_angle_3_deg11.161
r_dihedral_angle_1_deg7.967
r_long_range_B_refined7.797
r_long_range_B_other7.795
r_scangle_other6.259
r_scbond_it4.737
r_scbond_other4.735
r_mcangle_other4.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.6
r_dihedral_angle_4_deg15.847
r_dihedral_angle_3_deg11.161
r_dihedral_angle_1_deg7.967
r_long_range_B_refined7.797
r_long_range_B_other7.795
r_scangle_other6.259
r_scbond_it4.737
r_scbond_other4.735
r_mcangle_other4.63
r_mcangle_it4.616
r_mcbond_it3.796
r_mcbond_other3.782
r_angle_refined_deg1.502
r_angle_other_deg0.737
r_chiral_restr0.104
r_gen_planes_refined0.018
r_bond_refined_d0.014
r_gen_planes_other0.003
r_bond_other_d
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 Atoms245
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing