6TPX

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1-((1-acetylpiperidin-4-yl)methyl)-2-(4-hydroxy-3,5-dimethylphenyl)-N-methyl-1H-benzo[d]imidazole-5-carboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
othernon published structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29320% PEG6000, 0.2M NH4Cl, 0.1M tris pH8
Crystal Properties
Matthews coefficientSolvent content
1.935.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.868α = 90
b = 48.684β = 90
c = 57.629γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2011-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

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
11.4857.6395.60.025285.719018
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)
11.481.530.1287.23.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEnon published structure1.4837.2181897197895.4710.1560.15520.181419.439
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]
1.0470.195-1.242
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.14
r_dihedral_angle_3_deg12.753
r_dihedral_angle_4_deg12.108
r_dihedral_angle_1_deg5.76
r_lrange_it5.166
r_lrange_other5.164
r_scangle_it2.319
r_scangle_other2.318
r_mcangle_it1.618
r_mcangle_other1.618
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.14
r_dihedral_angle_3_deg12.753
r_dihedral_angle_4_deg12.108
r_dihedral_angle_1_deg5.76
r_lrange_it5.166
r_lrange_other5.164
r_scangle_it2.319
r_scangle_other2.318
r_mcangle_it1.618
r_mcangle_other1.618
r_scbond_it1.398
r_scbond_other1.397
r_angle_other_deg1.283
r_angle_refined_deg1.222
r_mcbond_it0.949
r_mcbond_other0.947
r_nbd_refined0.203
r_nbd_other0.189
r_nbtor_refined0.175
r_symmetry_nbd_other0.16
r_symmetry_nbd_refined0.124
r_xyhbond_nbd_refined0.106
r_symmetry_xyhbond_nbd_refined0.106
r_symmetry_nbtor_other0.08
r_chiral_restr0.065
r_gen_planes_refined0.006
r_bond_refined_d0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1061
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction