3EDH

Crystal structure of bone morphogenetic protein 1 protease domain in complex with partially bound DMSO

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	277	5% DMSO, pH 7.5, vapor diffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.499	α = 90
b = 59.093	β = 90
c = 69.451	γ = 90

Symmetry
Space Group	P 21 21 21

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 225 mm CCD		2007-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9999	SLS	X10SA

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.25	59.09	97.9	0.083	0.066	15.5	6	61581	60273		-3	15.7

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)	Redundancy	Number Unique Reflections (All)
	1.25	1.29	96.1		0.394	0.5	3.66	5.75	5271

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3EDI	1.25	44.99	60271	3014	97.88	0.142	0.14	0.172	RANDOM	15.07

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]
0.57			-0.39		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.53
r_dihedral_angle_4_deg	15.808
r_dihedral_angle_3_deg	13.396
r_sphericity_free	6.683
r_dihedral_angle_1_deg	6.418
r_sphericity_bonded	4.36
r_scangle_it	4.119
r_scbond_it	3.038
r_mcangle_it	2.38
r_rigid_bond_restr	1.74
r_mcbond_it	1.627
r_angle_refined_deg	1.578
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.313
r_nbd_refined	0.309
r_xyhbond_nbd_refined	0.212
r_symmetry_hbond_refined	0.183
r_metal_ion_refined	0.124
r_chiral_restr	0.106
r_bond_refined_d	0.013
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1693
Nucleic Acid Atoms
Solvent Atoms	410
Heterogen Atoms	29

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction