X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.5277Na cacodyrate, Mg(NO3)2, PEG 4000, GlcNAc, pH 6.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.448.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.777α = 105.19
b = 111.484β = 90.48
c = 118.432γ = 107.35
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2102007-01-28MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 3152006-11-29MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.000Photon FactoryAR-NW12A
2SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A0.97934, 0.97974, 0.96450Photon FactoryBL-5A

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
1,22.35097.80.05415.293226945613719535.8
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)
1,22.32.3897.50.2462.5213720

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.340.68137184686997.090.1730.170.231RANDOM35.174
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]
0.250.27-0.040.270.01-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.851
r_dihedral_angle_4_deg17.312
r_dihedral_angle_3_deg14.843
r_dihedral_angle_1_deg5.876
r_scangle_it2.401
r_scbond_it1.481
r_angle_refined_deg1.218
r_mcangle_it0.969
r_mcbond_it0.505
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.851
r_dihedral_angle_4_deg17.312
r_dihedral_angle_3_deg14.843
r_dihedral_angle_1_deg5.876
r_scangle_it2.401
r_scbond_it1.481
r_angle_refined_deg1.218
r_mcangle_it0.969
r_mcbond_it0.505
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23549
Nucleic Acid Atoms
Solvent Atoms1638
Heterogen Atoms85

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing