X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SOA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293.15100mM TRIS-HCl, 200mM sodium citrate, 30% PEG 400, 5mM DTT
Crystal Properties
Matthews coefficientSolvent content
3.1260.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.45α = 90
b = 75.45β = 90
c = 75.64γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702013-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.000Photon FactoryAR-NE3A

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
11.526.71000.0840.99813.37.240321
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)
11.51.581000.7210.7462.57

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 REPLACEMENTTHROUGHOUT1SOA1.526.738272201799.970.118020.116430.14795RANDOM24.851
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]
0.080.040.08-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.731
r_sphericity_free30.264
r_dihedral_angle_4_deg17.528
r_dihedral_angle_3_deg12.489
r_sphericity_bonded12.164
r_dihedral_angle_1_deg6.508
r_long_range_B_refined4.3
r_long_range_B_other3.647
r_scangle_other3.496
r_scbond_it3.347
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.731
r_sphericity_free30.264
r_dihedral_angle_4_deg17.528
r_dihedral_angle_3_deg12.489
r_sphericity_bonded12.164
r_dihedral_angle_1_deg6.508
r_long_range_B_refined4.3
r_long_range_B_other3.647
r_scangle_other3.496
r_scbond_it3.347
r_scbond_other3.346
r_rigid_bond_restr3.069
r_mcangle_other2.356
r_mcangle_it2.352
r_mcbond_it2.18
r_mcbond_other2.175
r_angle_refined_deg1.538
r_angle_other_deg0.896
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.008
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1376
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing