X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5290Internal tracking number 216858D10. JCSG+ screen condition D10: 0.2 M CaOAc2, 0.1 M MES cacodylate pH 6.5, 40% PEG300, MysmA.01365.d.A1 PW 28823 at 28.7 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.5652

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.14α = 90
b = 78.01β = 102.22
c = 155.43γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2010-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.541780

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
11.7541.2396.10.05720.477.53106123102002-324.209
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.885.20.483.24.577786

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2UVD1.7541.23106123101895510196.030.1520.1520.150.183RANDOM18.491
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]
-0.03-0.080.27-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.896
r_dihedral_angle_4_deg18.681
r_dihedral_angle_3_deg11.905
r_dihedral_angle_1_deg5.518
r_scangle_it4.273
r_scbond_it2.543
r_angle_refined_deg1.52
r_mcangle_it1.483
r_angle_other_deg0.997
r_mcbond_it0.882
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.896
r_dihedral_angle_4_deg18.681
r_dihedral_angle_3_deg11.905
r_dihedral_angle_1_deg5.518
r_scangle_it4.273
r_scbond_it2.543
r_angle_refined_deg1.52
r_mcangle_it1.483
r_angle_other_deg0.997
r_mcbond_it0.882
r_mcbond_other0.283
r_chiral_restr0.097
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7293
Nucleic Acid Atoms
Solvent Atoms878
Heterogen Atoms59

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction