X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YQWPDB ENTRY 1YQW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.1298VAPOR DIFFUSION, GLOVE BOX, 298K, PEG6000, MES, HEPES, DTT, DITHIONITE, PH 6.1
Crystal Properties
Matthews coefficientSolvent content
2.1141.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.53α = 90
b = 99.82β = 92.46
c = 182.42γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.4429.899.30.0629.393.67400635-320.6
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)
11.441.5397.60.6921.293.42

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 1YQW1.44253805362007599.330.143810.141640.18526RANDOM17.503
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]
1.560.28-0.38-1.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.043
r_dihedral_angle_4_deg15.829
r_dihedral_angle_3_deg12.495
r_dihedral_angle_1_deg5.744
r_scbond_it3.2
r_mcangle_it2.337
r_mcbond_it2.066
r_angle_refined_deg1.353
r_chiral_restr0.091
r_bond_refined_d0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.043
r_dihedral_angle_4_deg15.829
r_dihedral_angle_3_deg12.495
r_dihedral_angle_1_deg5.744
r_scbond_it3.2
r_mcangle_it2.337
r_mcbond_it2.066
r_angle_refined_deg1.353
r_chiral_restr0.091
r_bond_refined_d0.012
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_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 Atoms18454
Nucleic Acid Atoms
Solvent Atoms2022
Heterogen Atoms127

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing