1XHG | pdb_00001xhg

Crystal structure of a 40 kDa signalling protein from Porcine (SPP-40) at 2.89A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OWQ	PDB entry 1OWQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	298	25mM tris-HCl, 50mM NaCl, 20% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.75	α = 90
b = 66.454	β = 90
c = 107.652	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	293	IMAGE PLATE	MARRESEARCH	MIRROR	2004-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5412

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.89	56	90.7	0.13	3.3	7.3	10510	9476			36.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.89	3	87.1		0.542	1.3

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1OWQ	2.9	56	9476	9026	450	90.22	0.18	0.17911	0.17723	0.21765	RANDOM	28.47

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]
-0.91			-0.97		1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	21.681
r_scangle_it	5.032
r_dihedral_angle_1_deg	3.142
r_scbond_it	3.058
r_mcangle_it	2.528
r_angle_refined_deg	2.015
r_angle_other_deg	1.486
r_mcbond_it	1.355
r_symmetry_vdw_other	0.461
r_nbtor_other	0.393
r_symmetry_vdw_refined	0.356
r_nbd_refined	0.281
r_nbd_other	0.259
r_symmetry_hbond_refined	0.228
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.117
r_xyhbond_nbd_other	0.086
r_bond_refined_d	0.023
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.003
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_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	2875
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing