6TPZ

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 5-(1-(1,3-dimethoxypropan-2-yl)-5-morpholino-1H-benzo[d]imidazol-2-yl)-1,3-dimethylpyridin-2(1H)-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
othernot published

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293of 0.1 PCTP pH 8.0, 25% v/v PEG1500
Crystal Properties
Matthews coefficientSolvent content
1.8934.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.493α = 90
b = 49.533β = 90
c = 58.213γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97949DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.29949.5399.70.99930.55.928760
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.2991.3798.60.98711.2

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-VALUEnot published1.29937.72528705140799.5910.1930.19150.217617.491
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]
-0.2110.481-0.271
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.96
r_dihedral_angle_4_deg15.024
r_dihedral_angle_3_deg12.372
r_lrange_it5.362
r_lrange_other5.36
r_dihedral_angle_1_deg5.123
r_scangle_it2.296
r_scangle_other2.294
r_mcangle_it1.803
r_mcangle_other1.802
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.96
r_dihedral_angle_4_deg15.024
r_dihedral_angle_3_deg12.372
r_lrange_it5.362
r_lrange_other5.36
r_dihedral_angle_1_deg5.123
r_scangle_it2.296
r_scangle_other2.294
r_mcangle_it1.803
r_mcangle_other1.802
r_scbond_it1.362
r_scbond_other1.361
r_angle_other_deg1.188
r_angle_refined_deg1.144
r_mcbond_it1.048
r_mcbond_other1.042
r_nbd_other0.201
r_nbd_refined0.191
r_nbtor_refined0.169
r_symmetry_nbd_other0.16
r_symmetry_nbd_refined0.121
r_xyhbond_nbd_refined0.117
r_symmetry_xyhbond_nbd_refined0.099
r_symmetry_nbtor_other0.079
r_chiral_restr0.057
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1043
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling