X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4X1B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.6298PIPES-Na 0.1M pH 6.6, disodium malonate 8mM, PEG 3350 17%, glycerol 18%
Crystal Properties
Matthews coefficientSolvent content
3.8467.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.012α = 90
b = 155.752β = 90
c = 107.554γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.93001SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.85103.2999.70.0780.0840.0299.8827148
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.852.951000.7940.8480.2960.9058.1

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 REPLACEMENTTHROUGHOUT4X1B2.86103.2925317128397.480.15760.15370.2352RANDOM63.835
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]
-3.821.841.98
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded62.931
r_dihedral_angle_2_deg35.643
r_dihedral_angle_3_deg17.343
r_dihedral_angle_4_deg15.959
r_dihedral_angle_1_deg5.951
r_rigid_bond_restr3.851
r_angle_refined_deg1.381
r_angle_other_deg1.019
r_chiral_restr0.078
r_bond_refined_d0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded62.931
r_dihedral_angle_2_deg35.643
r_dihedral_angle_3_deg17.343
r_dihedral_angle_4_deg15.959
r_dihedral_angle_1_deg5.951
r_rigid_bond_restr3.851
r_angle_refined_deg1.381
r_angle_other_deg1.019
r_chiral_restr0.078
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4997
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms77

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERmodel building