X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P74PDB ENTRY 2P74

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.22930.8M phosphate , pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
238.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.128α = 90
b = 106.34β = 101.9
c = 47.61γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2008-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.0723ESRFID23-1

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
11.35093.60.04814.62.3100755
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)
11.31.3590.10.0965.92.39657

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 2P741.519.6562848332894.470.147190.14570.17519RANDOM9.853
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.05
r_dihedral_angle_3_deg13.255
r_dihedral_angle_4_deg12.012
r_scangle_it4.319
r_dihedral_angle_1_deg3.873
r_scbond_it2.882
r_mcangle_it2.538
r_mcbond_it1.743
r_angle_refined_deg1.63
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.05
r_dihedral_angle_3_deg13.255
r_dihedral_angle_4_deg12.012
r_scangle_it4.319
r_dihedral_angle_1_deg3.873
r_scbond_it2.882
r_mcangle_it2.538
r_mcbond_it1.743
r_angle_refined_deg1.63
r_nbtor_refined0.323
r_nbd_refined0.288
r_symmetry_vdw_refined0.23
r_symmetry_hbond_refined0.222
r_xyhbond_nbd_refined0.189
r_chiral_restr0.111
r_gen_planes_refined0.019
r_bond_refined_d0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3891
Nucleic Acid Atoms
Solvent Atoms787
Heterogen Atoms183

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling