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 60 MINUTES IN WELL SOLUTION WITH 0.005 M magnesium chloride, 0.005 M UMP, temperature 277K, VAPOR DIFFUSION, HANGING DROP, pH 6.00
Crystal Properties
Matthews coefficientSolvent content
2.9658.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.006α = 90
b = 134.006β = 90
c = 39.087γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 8-BMAPS8-BM

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
12.15098.90.07113.113.845396
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)
12.12.1597.60.3423.423.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2BDU2.132.1945392225798.90.1530.150.198RANDOM38.09
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]
-0.155-0.078-0.1550.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.322
r_dihedral_angle_4_deg20.609
r_dihedral_angle_3_deg14.187
r_dihedral_angle_1_deg5.492
r_scangle_it5.043
r_scbond_it3.867
r_mcangle_it1.918
r_angle_refined_deg1.316
r_mcbond_it1.141
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.322
r_dihedral_angle_4_deg20.609
r_dihedral_angle_3_deg14.187
r_dihedral_angle_1_deg5.492
r_scangle_it5.043
r_scbond_it3.867
r_mcangle_it1.918
r_angle_refined_deg1.316
r_mcbond_it1.141
r_nbtor_refined0.304
r_symmetry_vdw_refined0.204
r_nbd_refined0.193
r_symmetry_hbond_refined0.178
r_xyhbond_nbd_refined0.172
r_chiral_restr0.093
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4652
Nucleic Acid Atoms
Solvent Atoms848
Heterogen Atoms48

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing