X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AV5PDB ENTRY 1AV5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729840% PEG 20000, 0.1M Magnesium Acetate, 0.1M Sodium Acetate, 20 mM Tris, pH 7.0, 1mM EDTA, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1643.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.183α = 90
b = 65.298β = 109.75
c = 99.122γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDMARMOSAIC 325 mm CCDmirrors2006-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.975SSRLBL9-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.353895.20.1650.1155.33.42220961499862220.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.351.4577.70.2150.43.22.517208

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 1AV51.4537.96149986798398.780.179040.177440.20939RANDOM20.504
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.235
r_dihedral_angle_4_deg16.784
r_dihedral_angle_3_deg13.376
r_dihedral_angle_1_deg5.937
r_scangle_it2.851
r_scbond_it1.937
r_angle_refined_deg1.517
r_mcangle_it1.218
r_mcbond_it0.796
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.235
r_dihedral_angle_4_deg16.784
r_dihedral_angle_3_deg13.376
r_dihedral_angle_1_deg5.937
r_scangle_it2.851
r_scbond_it1.937
r_angle_refined_deg1.517
r_mcangle_it1.218
r_mcbond_it0.796
r_nbtor_refined0.308
r_symmetry_vdw_refined0.24
r_nbd_refined0.222
r_symmetry_hbond_refined0.153
r_xyhbond_nbd_refined0.139
r_chiral_restr0.099
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7277
Nucleic Acid Atoms
Solvent Atoms1068
Heterogen Atoms292

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALAdata scaling