X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BYNPDB ENTRY 2BYN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
119% PEG4000, 95 MM NA-CITRATE, PH 5.6, 19% ISOPROPANOL, 5% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.7154

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.251α = 90
b = 125.768β = 95.4
c = 257.001γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.77099.60.19.83.47326547.82
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)
12.72.851000.492.43.4

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 2BYN2.7258.270727219999.540.203270.20180.25059RANDOM40.515
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]
0.950.432.63-3.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.264
r_dihedral_angle_4_deg22.432
r_dihedral_angle_3_deg17.18
r_dihedral_angle_1_deg6.121
r_scangle_it1.542
r_angle_refined_deg1.108
r_mcangle_it1.031
r_scbond_it0.955
r_angle_other_deg0.897
r_mcbond_it0.555
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.264
r_dihedral_angle_4_deg22.432
r_dihedral_angle_3_deg17.18
r_dihedral_angle_1_deg6.121
r_scangle_it1.542
r_angle_refined_deg1.108
r_mcangle_it1.031
r_scbond_it0.955
r_angle_other_deg0.897
r_mcbond_it0.555
r_chiral_restr0.062
r_mcbond_other0.06
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16874
Nucleic Acid Atoms
Solvent Atoms307
Heterogen Atoms170

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing