1M4U

Crystal structure of Bone Morphogenetic Protein-7 (BMP-7) in complex with the secreted antagonist Noggin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.6 M disodium, 1.0 M monopotassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.8174.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.834α = 90
b = 99.834β = 90
c = 150.327γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-04-15MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-21.04888, 0.91987, 0.91957, 0.88557SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.426096.80.0542971328463-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.422.48399.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.4260.0527000144195.730.242430.240780.27303RANDOM60.096
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]
0.960.96-1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg24.632
r_scangle_it6.602
r_dihedral_angle_1_deg6.173
r_scbond_it4.116
r_mcangle_it3.227
r_angle_refined_deg3.034
r_mcbond_it1.78
r_angle_other_deg1.345
r_symmetry_vdw_other0.347
r_nbtor_other0.343
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg24.632
r_scangle_it6.602
r_dihedral_angle_1_deg6.173
r_scbond_it4.116
r_mcangle_it3.227
r_angle_refined_deg3.034
r_mcbond_it1.78
r_angle_other_deg1.345
r_symmetry_vdw_other0.347
r_nbtor_other0.343
r_symmetry_vdw_refined0.336
r_symmetry_hbond_refined0.31
r_nbd_other0.282
r_nbd_refined0.28
r_xyhbond_nbd_refined0.237
r_xyhbond_nbd_other0.226
r_chiral_restr0.201
r_symmetry_hbond_other0.062
r_bond_refined_d0.035
r_gen_planes_refined0.013
r_gen_planes_other0.003
r_bond_other_d0.002
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2485
Nucleic Acid Atoms
Solvent Atoms46
Heterogen Atoms28

Software

Software
Software NamePurpose
HKL-2000data collection
TRUNCATEdata reduction
MLPHAREphasing
REFMACrefinement
HKL-2000data reduction
CCP4data scaling