X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YCCPDB ENTRY 1YCC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.3293.1526 % PEG 8000, 100 mM Magnesium Chloride, 50 mM Sodium Chloride, 50 mM Sodium Cacodylate pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.4249.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.044α = 90
b = 55.317β = 90
c = 117.419γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray198.5CCDMARMOSAIC 225 mm CCD2011-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM141.13ESRFBM14

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
11.3995098.70.0440.04436.8114.34727347273-314.3
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)
11.3991.4290.60.2990.2992.3732.32082

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTPDB ENTRY 1YCC1.39930.194556695498.430.177420.176960.19848RANDOM17.163
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]
-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.133
r_dihedral_angle_4_deg17.532
r_dihedral_angle_3_deg13.652
r_dihedral_angle_1_deg5.779
r_scangle_it2.967
r_scbond_it1.977
r_mcangle_it1.309
r_angle_refined_deg1.238
r_mcbond_it0.686
r_chiral_restr0.287
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.133
r_dihedral_angle_4_deg17.532
r_dihedral_angle_3_deg13.652
r_dihedral_angle_1_deg5.779
r_scangle_it2.967
r_scbond_it1.977
r_mcangle_it1.309
r_angle_refined_deg1.238
r_mcbond_it0.686
r_chiral_restr0.287
r_bond_refined_d0.011
r_gen_planes_refined0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1688
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms230

Software

Software
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling