X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YDGPDB ENTRY 1YDG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629316% PEG 3350, 0.12M MgCl, 0.1M Bis pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0258.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.314α = 90
b = 73.331β = 90
c = 78.672γ = 90
Symmetry
Space GroupP 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A.9791NSLSX4A

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
12.62099.90.07323.46.81346913469-3
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)
12.62.691000.355.87.11309

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUTPDB ENTRY 1YDG2.620-3134671346773299.750.228710.228710.226210.2731RANDOM57.118
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]
1.091.49-2.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.025
r_dihedral_angle_4_deg23.972
r_dihedral_angle_3_deg16.442
r_dihedral_angle_1_deg6.215
r_scangle_it1.941
r_angle_refined_deg1.271
r_scbond_it1.151
r_mcangle_it1.101
r_angle_other_deg0.778
r_mcbond_it0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.025
r_dihedral_angle_4_deg23.972
r_dihedral_angle_3_deg16.442
r_dihedral_angle_1_deg6.215
r_scangle_it1.941
r_angle_refined_deg1.271
r_scbond_it1.151
r_mcangle_it1.101
r_angle_other_deg0.778
r_mcbond_it0.63
r_nbd_refined0.229
r_symmetry_vdw_other0.199
r_xyhbond_nbd_refined0.192
r_nbtor_refined0.179
r_nbd_other0.177
r_symmetry_vdw_refined0.151
r_symmetry_hbond_refined0.15
r_nbtor_other0.086
r_mcbond_other0.083
r_chiral_restr0.068
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2443
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing