2ESC | pdb_00002esc

Crystal structure of a 40 KDa protective signalling protein from Bovine (SPC-40) at 2.1 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	298	25mM TRIS-HCL, 50mM NACL, 19% ETHANOL , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.683	α = 90
b = 67.417	β = 90
c = 106.9	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	298	IMAGE PLATE	MARRESEARCH	MIRROR	2003-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	2.1	20	97.8	0.077	8.8		27796	27796

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	2.1	2.18	97.8		0.447	2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1LJY	2.1	20	27796	25190	1324	97.78	0.17573	0.17342	0.18	0.22021	0.19	RANDOM	36.152

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]
-0.22			-0.12		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	21.373
r_dihedral_angle_1_deg	4.874
r_scangle_it	4.25
r_scbond_it	2.58
r_angle_refined_deg	2.042
r_mcangle_it	1.982
r_angle_other_deg	1.494
r_mcbond_it	1.034
r_nbtor_other	0.561
r_nbd_refined	0.238
r_nbd_other	0.226
r_symmetry_vdw_refined	0.21
r_symmetry_vdw_other	0.209
r_chiral_restr	0.176
r_xyhbond_nbd_refined	0.159
r_symmetry_hbond_refined	0.145
r_xyhbond_nbd_other	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002
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_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	2874
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	72

Software

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