2POS | pdb_00002pos

Crystal Structure of sylvaticin, a new secreted protein from pythium sylvaticum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Sylvaticin C2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	40% PEG 2000MME, 10mM NiCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.22	α = 85.2
b = 46	β = 71.27
c = 55.73	γ = 74.63

Symmetry
Space Group	P 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	ADSC QUANTUM 4		2007-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

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	1.6	33	92	0.048	0.041	18.1	2	43901	40560	1		17.3

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)
	1.59	1.69	91.3		0.12	0.1	9.22	2	6468

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-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Sylvaticin C2	1.6	21.06	43341	40262	2024	92.9	0.152	0.152	0.15	0.16	0.187	RANDOM	19.769

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]
-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.403
r_dihedral_angle_3_deg	11.806
r_dihedral_angle_4_deg	6.956
r_dihedral_angle_1_deg	4.767
r_scangle_it	2.647
r_scbond_it	1.61
r_angle_refined_deg	1.11
r_mcangle_it	0.897
r_mcbond_it	0.497
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.403
r_dihedral_angle_3_deg	11.806
r_dihedral_angle_4_deg	6.956
r_dihedral_angle_1_deg	4.767
r_scangle_it	2.647
r_scbond_it	1.61
r_angle_refined_deg	1.11
r_mcangle_it	0.897
r_mcbond_it	0.497
r_nbtor_refined	0.307
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.169
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.109
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_metal_ion_refined	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2930
Nucleic Acid Atoms
Solvent Atoms	734
Heterogen Atoms	37

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
XDS	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.