X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CDR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH5.9293Complex made as 13uls of protein (24mgs/ml in 20mM HEPES, 100mM Na2SO4, 5mM MnCl2, pH 7.0) + 1.5ul of 40mM MgCl2 in 15% glycerol, 3ul of DNA (2mM duplex = 4mM monomer in water) + 2uls of 50% glycerol. Crystallisation buffer 9% PEG 5000mme, 80mM BisTris 5.9. 0.7ul complex + 0.8ul crystallisation buffer. CRYO:20% glycerol + 10.8% PEG 5000MME, 60mM BisTris 5.9,.
Crystal Properties
Matthews coefficientSolvent content
2.6653.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.28α = 90
b = 124.64β = 95.65
c = 155.24γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9762ESRFID29

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
12.62099.10.1020.9949.34.510748768.55
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)
12.62.6499.31.020.5271.34.6

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 REPLACEMENTTHROUGHOUT5CDR2.619.91107487524799.160.20140.19960.2362RANDOM63
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]
-5.84755.481-0.74996.5974
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion18.34
t_omega_torsion2.52
t_angle_deg1.03
t_bond_d0.009
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion18.34
t_omega_torsion2.52
t_angle_deg1.03
t_bond_d0.009
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21067
Nucleic Acid Atoms1567
Solvent Atoms468
Heterogen Atoms78

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing