4X1J | pdb_00004x1j

X-ray crystal structure of the dimeric BMP antagonist NBL1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1 MES/imidazole (pH 6.5) and 0.02M of several amino acids (sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine)

Crystal Properties
Matthews coefficient	Solvent content
2.55	56.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.665	α = 90
b = 59.665	β = 90
c = 145.018	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	CCD	MARMOSAIC 300 mm CCD		2013-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.979	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.5	55.18	99.68	23.5	12.3		9690

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.5	55.18	8674	964	99.68	0.22175	0.21576	0.2202	0.27315	0.2733	RANDOM	89.054

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]
0.25			0.25		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	43.6
r_dihedral_angle_2_deg	35.874
r_long_range_B_refined	16.68
r_long_range_B_other	16.676
r_dihedral_angle_3_deg	15.946
r_scangle_other	15.747
r_scbond_it	12.385
r_scbond_other	12.152
r_dihedral_angle_4_deg	10.462
r_mcangle_it	9.017
r_mcangle_other	9.013
r_mcbond_it	6.921
r_mcbond_other	6.921
r_dihedral_angle_1_deg	6.8
r_rigid_bond_restr	3.331
r_angle_refined_deg	1.523
r_angle_other_deg	1.011
r_chiral_restr	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.004
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_scangle_it
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1330
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing