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
2.2645.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.817α = 109.72
b = 53.63β = 91.19
c = 63.54γ = 94.81
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252010-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97908SSRFBL17U

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
11.945097.70.0912.13.737381
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)
11.942.0296.60.3393.73686

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 REPLACEMENTTHROUGHOUT1YH31.945035482189196.770.174620.172840.20834RANDOM34.627
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]
-1.720.070.512.380.33-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.264
r_dihedral_angle_4_deg19.672
r_dihedral_angle_3_deg13.398
r_dihedral_angle_1_deg5.53
r_scangle_it2.912
r_scbond_it1.815
r_angle_refined_deg1.198
r_mcangle_it1.084
r_angle_other_deg0.827
r_mcbond_it0.538
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.264
r_dihedral_angle_4_deg19.672
r_dihedral_angle_3_deg13.398
r_dihedral_angle_1_deg5.53
r_scangle_it2.912
r_scbond_it1.815
r_angle_refined_deg1.198
r_mcangle_it1.084
r_angle_other_deg0.827
r_mcbond_it0.538
r_mcbond_other0.136
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4086
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms44

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction