X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BYNpdb entry 2BYN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62910.1 M sodium citrate, 10% (w/v) PEG-1000, 24% (v/v) isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.8757.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.95α = 90
b = 145.472β = 90
c = 143.555γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.000ALS8.2.1

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
12.85501000.148.57.433957339572257.4
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)
12.852.951000.53514.77.23374

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2BYN2.88203395733817171498.80.2070.2050.237RANDOM39.971
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]
-0.440.98-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.332
r_dihedral_angle_4_deg27.657
r_dihedral_angle_3_deg16.508
r_dihedral_angle_1_deg6.43
r_scangle_it2.396
r_angle_refined_deg1.525
r_scbond_it1.401
r_mcangle_it1.061
r_mcbond_it0.629
r_symmetry_vdw_refined0.462
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.332
r_dihedral_angle_4_deg27.657
r_dihedral_angle_3_deg16.508
r_dihedral_angle_1_deg6.43
r_scangle_it2.396
r_angle_refined_deg1.525
r_scbond_it1.401
r_mcangle_it1.061
r_mcbond_it0.629
r_symmetry_vdw_refined0.462
r_symmetry_hbond_refined0.416
r_nbtor_refined0.318
r_nbd_refined0.225
r_xyhbond_nbd_refined0.148
r_chiral_restr0.079
r_bond_refined_d0.013
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8527
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms97

Software

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