X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YH3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42980.1M sodium acetate pH4.0, 0.2M ammonium acetate, 3% isopropanol, 15% PEG 10000, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2846

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.881α = 109.33
b = 53.511β = 90.53
c = 63.906γ = 94.83
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-05-08MSINGLE WAVELENGTH
21
31
41
51
61
71
81
91
101
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0630NSRRCBL13B1

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
11.915094.90.0956.73.137960
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)
11.911.9886.80.5412.53451

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 REPLACEMENTTHROUGHOUT1YH32.15029217148295.990.21830.21570.2663RANDOM38.668
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]
-4.590.03-0.223.243.953.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.105
r_dihedral_angle_4_deg17.152
r_dihedral_angle_3_deg14.154
r_dihedral_angle_1_deg5.326
r_scangle_it2.043
r_scbond_it1.343
r_angle_refined_deg1.199
r_mcangle_it0.72
r_mcbond_it0.385
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.105
r_dihedral_angle_4_deg17.152
r_dihedral_angle_3_deg14.154
r_dihedral_angle_1_deg5.326
r_scangle_it2.043
r_scbond_it1.343
r_angle_refined_deg1.199
r_mcangle_it0.72
r_mcbond_it0.385
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4062
Nucleic Acid Atoms
Solvent Atoms198
Heterogen Atoms40

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction