X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72910.1M sodium BICINE, pH 9, 0.2M ammonium sulfate, 2M sodium malonate pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
238.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.594α = 90
b = 41.206β = 109.3
c = 84.047γ = 90
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.826606PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.379.32490.30.0320.0440.022133.8206964
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3789.60.2860.2860.40.22.73.830039

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 REPLACEMENTTHROUGHOUT3HLJ1.369.462069362056090.240.1550.1510.192RANDOM16.645
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]
0.35-0.060.11-0.420.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.231
r_dihedral_angle_4_deg21.39
r_sphericity_free17.064
r_dihedral_angle_3_deg12.922
r_sphericity_bonded9.743
r_rigid_bond_restr9.493
r_dihedral_angle_1_deg7.195
r_angle_refined_deg2.286
r_chiral_restr0.182
r_bond_refined_d0.023
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.231
r_dihedral_angle_4_deg21.39
r_sphericity_free17.064
r_dihedral_angle_3_deg12.922
r_sphericity_bonded9.743
r_rigid_bond_restr9.493
r_dihedral_angle_1_deg7.195
r_angle_refined_deg2.286
r_chiral_restr0.182
r_bond_refined_d0.023
r_gen_planes_refined0.017
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8191
Nucleic Acid Atoms
Solvent Atoms1013
Heterogen Atoms204

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction
MOLREPphasing