X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B4G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62930.1M Sodium Citrate buffer, 1.5-2.5 M Sodium Malonate
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.914α = 90
b = 146.979β = 90
c = 66.491γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 210r2012-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0000Photon FactoryAR-NE3A

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
11.7950990.0777.111.1128274
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8398.57.1

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 REPLACEMENTTHROUGHOUT2B4G1.7934.98120628637698.790.167530.165960.19762RANDOM22.277
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]
0.010.05-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.604
r_dihedral_angle_4_deg16.705
r_dihedral_angle_3_deg11.741
r_dihedral_angle_1_deg5.563
r_long_range_B_refined3.986
r_long_range_B_other3.761
r_angle_other_deg3.575
r_scangle_other2.109
r_mcangle_it1.513
r_mcangle_other1.513
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.604
r_dihedral_angle_4_deg16.705
r_dihedral_angle_3_deg11.741
r_dihedral_angle_1_deg5.563
r_long_range_B_refined3.986
r_long_range_B_other3.761
r_angle_other_deg3.575
r_scangle_other2.109
r_mcangle_it1.513
r_mcangle_other1.513
r_scbond_it1.284
r_scbond_other1.283
r_angle_refined_deg1.181
r_mcbond_it0.908
r_mcbond_other0.907
r_chiral_restr0.068
r_gen_planes_refined0.012
r_gen_planes_other0.011
r_bond_refined_d0.006
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 Atoms9552
Nucleic Acid Atoms
Solvent Atoms752
Heterogen Atoms201

Software

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