X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JYK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5289200 nl of 10 mg/ml protein in 10 mM HEPES pH 7.5, 500 mM NaCl, 5 mM dihydrouracil was mixed with 200 nl 50 mM Ammonium Slufate, 50 mM BIS-TRIS, pH 6.5, 30% (v/v) Pentaerythirtol ethoxylate and suspended over a reservoir of 1.5M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.2645.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.892α = 88.37
b = 55.672β = 88.8
c = 85.242γ = 62.37
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium Lenses2014-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
12.2750.0197.50.05614.62.28177737742
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)
12.272.31910.551.672.1

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 REPLACEMENTTHROUGHOUT4JYK2.2750.0135540182797.510.195660.194070.22539RANDOM52.064
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]
2.31-2.29-1.92-1.390.74-2.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.706
r_dihedral_angle_3_deg15.122
r_dihedral_angle_4_deg14.276
r_dihedral_angle_1_deg4.989
r_long_range_B_refined4.03
r_long_range_B_other3.975
r_scangle_other2.578
r_mcangle_it2.093
r_mcangle_other2.093
r_scbond_it1.558
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.706
r_dihedral_angle_3_deg15.122
r_dihedral_angle_4_deg14.276
r_dihedral_angle_1_deg4.989
r_long_range_B_refined4.03
r_long_range_B_other3.975
r_scangle_other2.578
r_mcangle_it2.093
r_mcangle_other2.093
r_scbond_it1.558
r_scbond_other1.558
r_angle_refined_deg1.354
r_angle_other_deg1.351
r_mcbond_it1.326
r_mcbond_other1.326
r_chiral_restr0.078
r_gen_planes_refined0.014
r_gen_planes_other0.012
r_bond_refined_d0.01
r_bond_other_d0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6133
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
PDB_EXTRACTdata extraction
HKL-3000data scaling
HKL-3000phasing