5MGM

Crystal Structure of BAZ2A bromodomain in complex with acetophenone derivative 4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LZ2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527720% PEG3350, 0.2 M MgCl2
Crystal Properties
Matthews coefficientSolvent content
3.4464.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.861α = 90
b = 94.861β = 90
c = 32.75γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.00ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.827.3899.50.3180.9847.19.84298
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.951001.3470.6998.7

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 REPLACEMENTFREE R-VALUE4LZ22.827.38410918799.10.21950.21810.2518RANDOM41.931
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]
13.1613.16-26.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.239
r_dihedral_angle_4_deg13.716
r_dihedral_angle_3_deg10.968
r_dihedral_angle_1_deg4
r_mcangle_it2.094
r_mcbond_it1.147
r_mcbond_other1.13
r_angle_refined_deg0.873
r_angle_other_deg0.676
r_chiral_restr0.047
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.239
r_dihedral_angle_4_deg13.716
r_dihedral_angle_3_deg10.968
r_dihedral_angle_1_deg4
r_mcangle_it2.094
r_mcbond_it1.147
r_mcbond_other1.13
r_angle_refined_deg0.873
r_angle_other_deg0.676
r_chiral_restr0.047
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms829
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms16

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction