X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BDUpdb entry 2BDU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6277PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.005 M BIS TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (20-25% PEG 8K, 0.10 M PIPES PH 6.5) CRYSTALS SOAKED FOR 15 MINUTES IN WELL SOLUTION WITH 0.005 M magnesium chloride, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.9858.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.343α = 90
b = 134.343β = 90
c = 39.152γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER PROTEUM-RMONTEL OPTICS2006-01-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
12.2567.171000.100620.6117.8237523
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)
12.252.31000.63712.676.472423

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2BDU2.2567.1737505189999.9550.1580.1580.15480.2193RANDOM35.072
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]
0.2040.1020.204-0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.774
r_dihedral_angle_4_deg22.555
r_dihedral_angle_3_deg15.516
r_scangle_it5.969
r_dihedral_angle_1_deg5.893
r_scbond_it4.389
r_mcangle_it2.236
r_angle_refined_deg1.474
r_mcbond_it1.291
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.774
r_dihedral_angle_4_deg22.555
r_dihedral_angle_3_deg15.516
r_scangle_it5.969
r_dihedral_angle_1_deg5.893
r_scbond_it4.389
r_mcangle_it2.236
r_angle_refined_deg1.474
r_mcbond_it1.291
r_nbtor_refined0.309
r_symmetry_vdw_refined0.249
r_xyhbond_nbd_refined0.212
r_nbd_refined0.207
r_symmetry_hbond_refined0.193
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4652
Nucleic Acid Atoms
Solvent Atoms815
Heterogen Atoms38

Software

Software
Software NamePurpose
SAINTdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SADABSdata scaling
MOLREPphasing