X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BEM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP297Protein: 8.0 mg/ml, 0.01 M Tris HCl (pH 8.3); Screen: JCSG+ H9 (Qiagen),0.2 M AmSO4, 0.1 M Bis-Tris (pH 5.5), 25% (w/v) PEG3350.
Crystal Properties
Matthews coefficientSolvent content
2.7254.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.575α = 90
b = 139.712β = 90
c = 90.591γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2016-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G.978APS21-ID-G

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
11.13094.80.07921.66.7148923
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)
11.11.1266.90.7491.63.9

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 REPLACEMENTTHROUGHOUT2BEM1.129.15141504738295.50.1290.1290.145RANDOM13.23
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]
-0.3-0.150.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.238
r_sphericity_free27.415
r_dihedral_angle_4_deg11.085
r_dihedral_angle_3_deg9.951
r_dihedral_angle_1_deg6.609
r_sphericity_bonded6.34
r_long_range_B_refined3.149
r_long_range_B_other1.766
r_angle_refined_deg1.428
r_rigid_bond_restr0.939
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.238
r_sphericity_free27.415
r_dihedral_angle_4_deg11.085
r_dihedral_angle_3_deg9.951
r_dihedral_angle_1_deg6.609
r_sphericity_bonded6.34
r_long_range_B_refined3.149
r_long_range_B_other1.766
r_angle_refined_deg1.428
r_rigid_bond_restr0.939
r_angle_other_deg0.926
r_scangle_other0.877
r_scbond_it0.751
r_scbond_other0.748
r_mcangle_it0.699
r_mcangle_other0.699
r_mcbond_it0.525
r_mcbond_other0.523
r_chiral_restr0.086
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2534
Nucleic Acid Atoms
Solvent Atoms620
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing