2QCW | pdb_00002qcw

Crystal Structure of Bone Morphogenetic Protein-6 (BMP-6)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LXI	BMP-7 ligand monomer taken from PDB entry 1lxi

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	296	15% 2-methyl-2,4-pentanediol (MPD), 0.2 M Tri-Na Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
4.02	69.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.446	α = 90
b = 97.446	β = 90
c = 87.377	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2006-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.98	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.49	42.5	93	0.053	12.6	5.3		16679

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.59	57.2		0.437		2.8	1092

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	BMP-7 ligand monomer taken from PDB entry 1lxi	2.49	42.5	15112	808	92.7	0.23486	0.23285	0.25	0.27589	0.3	RANDOM	63.308

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]
-1.59	-0.8		-1.59		2.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.524
r_dihedral_angle_4_deg	22.308
r_dihedral_angle_3_deg	19.713
r_dihedral_angle_1_deg	6.809
r_scangle_it	2.293
r_scbond_it	1.41
r_angle_refined_deg	1.396
r_mcangle_it	1.225
r_mcbond_it	0.679
r_nbtor_refined	0.314
r_nbd_refined	0.226
r_symmetry_vdw_refined	0.205
r_xyhbond_nbd_refined	0.174
r_symmetry_hbond_refined	0.156
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
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 Atoms	Number
Protein Atoms	1646
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing