3EDG

Crystal structure of bone morphogenetic protein 1 protease domain

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.432	α = 90
b = 57.26	β = 90
c = 68.8	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	1.27	68.79	98.3	0.091	0.078	17.1	6.6	58437	57443	-3	-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)
	1.27	1.31	86.3		0.471	0.484	2.9	3.9	4393

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.27	44.02	58437	57442	2873	98.29	0.146	0.144	0.177	RANDOM	14.322

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]
0.19			0.18		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.203
r_dihedral_angle_4_deg	16.795
r_dihedral_angle_3_deg	13.344
r_dihedral_angle_1_deg	5.649
r_sphericity_free	4.902
r_scangle_it	3.867
r_sphericity_bonded	3.232
r_scbond_it	2.822
r_mcangle_it	2.028
r_rigid_bond_restr	1.643
r_mcbond_it	1.43
r_angle_refined_deg	1.375
r_nbtor_refined	0.314
r_nbd_refined	0.293
r_symmetry_vdw_refined	0.231
r_xyhbond_nbd_refined	0.18
r_symmetry_hbond_refined	0.168
r_metal_ion_refined	0.104
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1610
Nucleic Acid Atoms
Solvent Atoms	426
Heterogen Atoms	5

Software

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