X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YMLPDB ENTRY 2YML

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18pH 8
Crystal Properties
Matthews coefficientSolvent content
2.0339.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.17α = 90
b = 68.27β = 90
c = 283.2γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
12.1636.8699.90.0912.4646129
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)
12.162.162.20.622.56.2

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 2YML2.1636.8643714233099.870.185790.18220.25367RANDOM42.544
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]
0.280.05-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.357
r_dihedral_angle_3_deg16.58
r_dihedral_angle_4_deg14.657
r_mcangle_it8.339
r_scbond_it7.388
r_mcbond_it6.339
r_dihedral_angle_1_deg5.997
r_angle_refined_deg1.51
r_chiral_restr0.111
r_bond_refined_d0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.357
r_dihedral_angle_3_deg16.58
r_dihedral_angle_4_deg14.657
r_mcangle_it8.339
r_scbond_it7.388
r_mcbond_it6.339
r_dihedral_angle_1_deg5.997
r_angle_refined_deg1.51
r_chiral_restr0.111
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms6936
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement