3MDY

Crystal structure of the cytoplasmic domain of the bone morphogenetic protein receptor type-1B (BMPR1B) in complex with FKBP12 and LDN-193189


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H9RPDB ENTRY: 3H9R CHAIN A, and CHAIN B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7277.1520% PEG 3350, 0.2M Na Malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
2.3848.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.41α = 90
b = 80.01β = 90
c = 183.33γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Kirkpatrick Baez bimorph mirror pair2010-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
12.0548.7998.90.128.65.4610556096825
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)
2.052.1698.30.5212.13.78618

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 REPLACEMENTTHROUGHOUTPDB ENTRY: 3H9R CHAIN A, and CHAIN B2.0544.656096857883308599.540.20420.201450.2548RANDOM26.029
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]
-0.732.56-1.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.449
r_dihedral_angle_4_deg19.707
r_dihedral_angle_3_deg14.462
r_scangle_it9.839
r_scbond_it7.434
r_dihedral_angle_1_deg6.079
r_mcangle_it5.486
r_mcbond_it3.706
r_angle_refined_deg1.422
r_angle_other_deg0.926
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.449
r_dihedral_angle_4_deg19.707
r_dihedral_angle_3_deg14.462
r_scangle_it9.839
r_scbond_it7.434
r_dihedral_angle_1_deg6.079
r_mcangle_it5.486
r_mcbond_it3.706
r_angle_refined_deg1.422
r_angle_other_deg0.926
r_mcbond_other0.894
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms6727
Nucleic Acid Atoms
Solvent Atoms687
Heterogen Atoms62

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling