X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OFM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529320% (w/v) PEG10000, 0.1M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.2344.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.719α = 90
b = 114.139β = 90.04
c = 133.75γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.786.8299.80.213.83.3153463
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7399.70.322.13.1

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 REPLACEMENTTHROUGHOUT3OFM1.786.8145745752999.70.264590.263210.29116RANDOM15.532
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]
-0.86-0.180.30.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.055
r_dihedral_angle_4_deg20.884
r_dihedral_angle_3_deg13.861
r_dihedral_angle_1_deg6.343
r_long_range_B_refined3.873
r_long_range_B_other3.848
r_scangle_other2.743
r_mcangle_it2.229
r_mcangle_other2.229
r_scbond_it1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.055
r_dihedral_angle_4_deg20.884
r_dihedral_angle_3_deg13.861
r_dihedral_angle_1_deg6.343
r_long_range_B_refined3.873
r_long_range_B_other3.848
r_scangle_other2.743
r_mcangle_it2.229
r_mcangle_other2.229
r_scbond_it1.78
r_scbond_other1.78
r_mcbond_it1.45
r_mcbond_other1.44
r_angle_refined_deg1.372
r_angle_other_deg0.932
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10757
Nucleic Acid Atoms
Solvent Atoms552
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing