6ZB3 | pdb_00006zb3

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH GSK620


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29330%w/v PEG3350, 0.1M NaAc, 0.1M MES, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.1442.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.092α = 90
b = 44.337β = 90
c = 78.448γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9626ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.41978.44896.60.0550.0660.02621.45.92433924339
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.421.580.30.1080.1080.1390.0676.64

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEin house structure1.41938.59924288124496.3810.1640.16310.170.18160.1912.94
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]
0.1020.13-0.232
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.82
r_dihedral_angle_3_deg10.467
r_dihedral_angle_4_deg9.252
r_dihedral_angle_1_deg5.803
r_lrange_it5.019
r_lrange_other5.018
r_scangle_it1.453
r_scangle_other1.452
r_angle_other_deg1.264
r_angle_refined_deg1.206
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.82
r_dihedral_angle_3_deg10.467
r_dihedral_angle_4_deg9.252
r_dihedral_angle_1_deg5.803
r_lrange_it5.019
r_lrange_other5.018
r_scangle_it1.453
r_scangle_other1.452
r_angle_other_deg1.264
r_angle_refined_deg1.206
r_mcangle_it1.205
r_mcangle_other1.204
r_scbond_it0.866
r_scbond_other0.865
r_mcbond_it0.683
r_mcbond_other0.682
r_nbd_refined0.191
r_nbtor_refined0.175
r_symmetry_nbd_other0.164
r_nbd_other0.154
r_xyhbond_nbd_refined0.105
r_symmetry_nbd_refined0.095
r_symmetry_xyhbond_nbd_refined0.093
r_symmetry_nbtor_other0.079
r_chiral_restr0.062
r_gen_planes_refined0.005
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 Atoms1062
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling