3P1D

Crystal structure of the bromodomain of human CREBBP in complex with N-Methyl-2-pyrrolidone (NMP)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DWY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2M KSCN 20% PEG3350 5% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0138.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.549α = 90
b = 121.549β = 90
c = 40.23γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2009-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.542

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.8619.7699.90.0670.06711.83.71863218613
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.961000.6290.6291.23.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3DWY1.8619.76186091766594299.990.169520.1670.21819RANDOM28.168
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]
-0.87-0.43-0.871.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.004
r_dihedral_angle_4_deg15.364
r_dihedral_angle_3_deg14.682
r_scangle_it8.686
r_scbond_it7.334
r_dihedral_angle_1_deg6.117
r_mcangle_it4.901
r_mcbond_it3.456
r_angle_refined_deg1.5
r_mcbond_other1.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.004
r_dihedral_angle_4_deg15.364
r_dihedral_angle_3_deg14.682
r_scangle_it8.686
r_scbond_it7.334
r_dihedral_angle_1_deg6.117
r_mcangle_it4.901
r_mcbond_it3.456
r_angle_refined_deg1.5
r_mcbond_other1.126
r_angle_other_deg0.952
r_chiral_restr0.085
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1859
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms18

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction