X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.525% PEG 4K, 0.1 M HEPES, PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.764α = 89.95
b = 85.731β = 97.33
c = 117.318γ = 106.64
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

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
12.055895.80.0613.9216854525.6
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)
12.052.1695.40.262.52

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 2BYN2.0547.73161270502594.50.2170.2160.258RANDOM32.39
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]
5.242.240.25-1.310.3-2.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.891
r_dihedral_angle_4_deg20.581
r_dihedral_angle_3_deg15.408
r_dihedral_angle_1_deg6.392
r_angle_refined_deg1.162
r_scangle_it0.981
r_angle_other_deg0.716
r_scbond_it0.675
r_mcangle_it0.417
r_mcbond_it0.352
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.891
r_dihedral_angle_4_deg20.581
r_dihedral_angle_3_deg15.408
r_dihedral_angle_1_deg6.392
r_angle_refined_deg1.162
r_scangle_it0.981
r_angle_other_deg0.716
r_scbond_it0.675
r_mcangle_it0.417
r_mcbond_it0.352
r_symmetry_vdw_other0.244
r_symmetry_hbond_refined0.19
r_nbd_other0.186
r_nbd_refined0.175
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.165
r_nbtor_other0.081
r_symmetry_vdw_refined0.081
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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 Atoms16324
Nucleic Acid Atoms
Solvent Atoms1559
Heterogen Atoms250

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing