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 5 MINUTES IN WELL SOLUTION WITH 0.001 M Lead(II) Acetate, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
358.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.549α = 90
b = 134.549β = 90
c = 39.226γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER PROTEUM-RMONTEL OPTICS2005-12-27SINGLE 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
12.3567.271000.095926.0524.1933118
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)
12.352.41000.53023.456.762063

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 2BDU2.3567.2733098166899.9610.1530.1530.14940.2293RANDOM38.913
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]
0.1720.0860.172-0.257
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.22
r_dihedral_angle_4_deg24.168
r_dihedral_angle_3_deg16.393
r_dihedral_angle_1_deg6.283
r_scangle_it3.775
r_scbond_it2.498
r_angle_refined_deg1.507
r_mcangle_it1.343
r_mcbond_it0.765
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.22
r_dihedral_angle_4_deg24.168
r_dihedral_angle_3_deg16.393
r_dihedral_angle_1_deg6.283
r_scangle_it3.775
r_scbond_it2.498
r_angle_refined_deg1.507
r_mcangle_it1.343
r_mcbond_it0.765
r_nbtor_refined0.306
r_symmetry_hbond_refined0.276
r_symmetry_vdw_refined0.209
r_nbd_refined0.207
r_xyhbond_nbd_refined0.196
r_chiral_restr0.112
r_metal_ion_refined0.104
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 Atoms862
Heterogen Atoms32

Software

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