3E07 | pdb_00003e07

Crystal structure of spatzle cystine knot

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BTG	PDB ENTRIES 1BTG, 1SG1, 1BET, 1SGF
experimental model	PDB	1SG1	PDB ENTRIES 1BTG, 1SG1, 1BET, 1SGF
experimental model	PDB	1BET	PDB ENTRIES 1BTG, 1SG1, 1BET, 1SGF
experimental model	PDB	1SGF	PDB ENTRIES 1BTG, 1SG1, 1BET, 1SGF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	50mM TRIS/HCl, 20% PEG 3350, 10mM betaine monohydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.8	α = 90
b = 58.98	β = 90
c = 62.21	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	180	CCD	MARMOSAIC 225 mm CCD	mirrors	2008-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91840	BESSY	14.1

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	2.4	30	99.1	0.055	0.062	16.49	4.712	7988	7919	2	-3	59.222

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	2.4	2.5	99.9		0.631	0.706	2.5	4.88	886

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-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 ENTRIES 1BTG, 1SG1, 1BET, 1SGF	2.4	19.83	7988	7919	610	99.2	0.222	0.2253	0.265	0.2698	RANDOM	64.958

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]
-8.8			-3.12		11.92

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	27.3
c_scangle_it	12
c_mcangle_it	9.6
c_scbond_it	8.25
c_mcbond_it	6.86
c_angle_deg	1.4
c_improper_angle_d	0.73
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1417
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	6

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction