X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2TRXPDB entry 2TRX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1COUNTER-DIFFUSION3.527760% (v/v) MPD, Ac2Cu 1mM, AcNa 15mM, HEPES 15 mM pH 6.9, pH 3.5, Counterdiffusion, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7955.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.727α = 90
b = 102.727β = 90
c = 42.865γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 6000Montel Optics2006-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEOTHER1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.651.3699.80.07879.087.288147814751.288
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.651000.31612.637.28464

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2TRX2.644.58147807737099.180.2220.2220.2190.284RANDOM43.014
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]
-0.48-0.24-0.480.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.224
r_dihedral_angle_3_deg16.628
r_dihedral_angle_4_deg15.798
r_dihedral_angle_1_deg6.349
r_mcangle_it1.954
r_scangle_it1.636
r_angle_refined_deg1.427
r_mcbond_it1.193
r_scbond_it1.142
r_symmetry_hbond_refined0.366
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.224
r_dihedral_angle_3_deg16.628
r_dihedral_angle_4_deg15.798
r_dihedral_angle_1_deg6.349
r_mcangle_it1.954
r_scangle_it1.636
r_angle_refined_deg1.427
r_mcbond_it1.193
r_scbond_it1.142
r_symmetry_hbond_refined0.366
r_nbtor_refined0.309
r_nbd_refined0.223
r_xyhbond_nbd_refined0.21
r_symmetry_vdw_refined0.181
r_chiral_restr0.083
r_bond_refined_d0.014
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1636
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata reduction
SAINTdata scaling
SADABSdata scaling
XPREPdata reduction
AMoREphasing
Cootmodel building
MolProbitymodel building