4AWL

The NF-Y transcription factor is structurally and functionally a sequence specific histone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N1JPDB ENTRY 1N1J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5VAPOUR DIFFUSION METHOD , HANGING DROP, 20-24% PEG3350, 100 MM MES OR CACODYLATE BUFFER, PH 6.5, 50 MM NAF. T ROOM.
Crystal Properties
Matthews coefficientSolvent content
2.5651.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.7α = 90
b = 62.56β = 90
c = 139.68γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9,1.0ESRFID29

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
13.0862.5694.90.0617.45.289073
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)
13.083.2576.90.174.43.5

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 1N1J3.0835.4684484181000.194180.191330.24971RANDOM79.475
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]
8.15-0.55-7.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.568
r_dihedral_angle_3_deg23.756
r_dihedral_angle_4_deg18.478
r_dihedral_angle_1_deg5.831
r_scangle_it1.969
r_angle_refined_deg1.751
r_scbond_it1.183
r_mcangle_it0.853
r_mcbond_it0.42
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.568
r_dihedral_angle_3_deg23.756
r_dihedral_angle_4_deg18.478
r_dihedral_angle_1_deg5.831
r_scangle_it1.969
r_angle_refined_deg1.751
r_scbond_it1.183
r_mcangle_it0.853
r_mcbond_it0.42
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.006
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_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 Atoms1928
Nucleic Acid Atoms1019
Solvent Atoms2
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing