3IQO | pdb_00003iqo

1.5 angstrom X-ray structure of bovine Ca(2+)-S100B

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop	6.3	295	25% PEG3350, 7.5mM CaCl2, 100mM Cacodylate buffer, pH 6.3, sitting drop, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.637	α = 90
b = 35.044	β = 92.62
c = 58.113	γ = 90

Symmetry
Space Group	C 1 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		2009-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97	SSRL	BL12-2

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	1.5	32.63	89.4	0.061	20.1	2.6		26110

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	1.5	1.55	72.7		0.247		1.5	2097

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	PDB entry 1MHO	1.5	32.63	26069	1323	89.07	0.202	0.2	0.2006	0.242	0.2428	RANDOM	32.557

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]
-0.96		0.08	0.65		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.981
r_dihedral_angle_4_deg	23.563
r_dihedral_angle_3_deg	12.452
r_dihedral_angle_1_deg	4.338
r_scangle_it	3.807
r_scbond_it	2.391
r_angle_refined_deg	1.333
r_mcangle_it	1.216
r_mcbond_it	0.817
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.291
r_symmetry_hbond_refined	0.235
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.2
r_chiral_restr	0.099
r_metal_ion_refined	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1420
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction