2QJB

Crystal structure analysis of BMP-2 in complex with BMPR-IA variant IA/IB


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1REWpdb entry 1REW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82980.8M K Na phosphate, 25% ethylene glycol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8857.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.175α = 90
b = 104.175β = 90
c = 100.012γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

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
12.531.2799.90.0830.08311.25.232136021360
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)
12.52.5999.90.5640.5642.85.32

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 1REW2.531.272129020259109799.790.206820.203880.26259RANDOM81.516
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]
-1.1-0.55-1.11.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.72
r_dihedral_angle_3_deg20.577
r_dihedral_angle_4_deg18.482
r_dihedral_angle_1_deg6.772
r_scangle_it2.5
r_scbond_it1.634
r_angle_refined_deg1.567
r_mcangle_it1.338
r_mcbond_it0.729
r_symmetry_hbond_refined0.396
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.72
r_dihedral_angle_3_deg20.577
r_dihedral_angle_4_deg18.482
r_dihedral_angle_1_deg6.772
r_scangle_it2.5
r_scbond_it1.634
r_angle_refined_deg1.567
r_mcangle_it1.338
r_mcbond_it0.729
r_symmetry_hbond_refined0.396
r_symmetry_vdw_refined0.345
r_nbtor_refined0.334
r_nbd_refined0.275
r_xyhbond_nbd_refined0.21
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2972
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing