X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DROpdb entry 1DRO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729820% PEG4000, 100mM HEPES, 5% glycerol, 5mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1242.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.751α = 90
b = 36.601β = 90
c = 113.708γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315bent-flat Si-mirror (Rh coated)2004-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90020APS14-BM-C

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
11.92593.10.05518.45.89223
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)
1.91.9791.30.291

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 1DRO1.9120874443892.850.210280.20930.23014RANDOM20.745
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]
-0.661.46-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.551
r_dihedral_angle_4_deg21.242
r_dihedral_angle_3_deg13.833
r_dihedral_angle_1_deg5.971
r_scangle_it5.251
r_scbond_it3.248
r_mcangle_it2.023
r_mcbond_it1.844
r_angle_refined_deg1.68
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.551
r_dihedral_angle_4_deg21.242
r_dihedral_angle_3_deg13.833
r_dihedral_angle_1_deg5.971
r_scangle_it5.251
r_scbond_it3.248
r_mcangle_it2.023
r_mcbond_it1.844
r_angle_refined_deg1.68
r_nbtor_refined0.3
r_symmetry_hbond_refined0.284
r_symmetry_vdw_refined0.245
r_nbd_refined0.22
r_xyhbond_nbd_refined0.176
r_chiral_restr0.119
r_bond_refined_d0.017
r_gen_planes_refined0.008
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 Atoms927
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms5

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction