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% PEG10000, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2745.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.87α = 109.56
b = 53.658β = 90.95
c = 63.562γ = 94.73
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252010-03-31MSINGLE WAVELENGTH
21
31
41
51
61
71
81
91
101
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
11.655095.90.07114.43.959566
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)
11.651.7195.50.39945944

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 REPLACEMENTTHROUGHOUT1YH31.655059515300695.340.18120.17980.2088RANDOM33.447
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]
-1.17-0.020.110.410.611.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.864
r_dihedral_angle_4_deg14.631
r_dihedral_angle_3_deg12.826
r_dihedral_angle_1_deg5.512
r_scangle_it3.022
r_scbond_it1.961
r_angle_refined_deg1.282
r_mcangle_it1.145
r_angle_other_deg0.816
r_mcbond_it0.574
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.864
r_dihedral_angle_4_deg14.631
r_dihedral_angle_3_deg12.826
r_dihedral_angle_1_deg5.512
r_scangle_it3.022
r_scbond_it1.961
r_angle_refined_deg1.282
r_mcangle_it1.145
r_angle_other_deg0.816
r_mcbond_it0.574
r_mcbond_other0.157
r_chiral_restr0.138
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4082
Nucleic Acid Atoms
Solvent Atoms368
Heterogen Atoms34

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction