X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BVQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5281Protein was concentrated to 2.1 mg/mL in 100 mM NaCl and 50 mM HEPES pH 7.5; reservoir was 20% PEG 3350, 0.2 M magnesium acetate, 20 mM HEPES pH 6.8 with the Silver Bullets Bio C1 condition of additives; 200 nL of protein added to 90 nL of reservoir and 10 nL of microseeds.
Crystal Properties
Matthews coefficientSolvent content
2.652.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.576α = 96.47
b = 85.661β = 114.94
c = 87.23γ = 111.77
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95370Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.446.397.5243.965127
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4683.13.83.8

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 REPLACEMENTTHROUGHOUT4BVQ2.441.561420326696.840.196440.194350.23633RANDOM26.693
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]
2.05-0.6-0.71-0.28-0.350.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.353
r_dihedral_angle_4_deg23.669
r_dihedral_angle_3_deg14.13
r_long_range_B_refined8.546
r_long_range_B_other8.546
r_dihedral_angle_1_deg6.975
r_scangle_other5.62
r_mcangle_it5.09
r_mcangle_other5.09
r_scbond_it3.701
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.353
r_dihedral_angle_4_deg23.669
r_dihedral_angle_3_deg14.13
r_long_range_B_refined8.546
r_long_range_B_other8.546
r_dihedral_angle_1_deg6.975
r_scangle_other5.62
r_mcangle_it5.09
r_mcangle_other5.09
r_scbond_it3.701
r_scbond_other3.694
r_mcbond_it3.265
r_mcbond_other3.262
r_angle_refined_deg1.682
r_angle_other_deg1.649
r_chiral_restr0.089
r_bond_refined_d0.015
r_bond_other_d0.01
r_gen_planes_refined0.01
r_gen_planes_other0.008
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 Atoms10286
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing