2QF9 | pdb_00002qf9

Crystal structure of putative secreted protein DUF305 from Streptomyces coelicolor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	1M Bis-Tris pH 5.5, 50% PEG 3350, 1M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.903	α = 90
b = 52.756	β = 104.43
c = 57.273	γ = 90

Symmetry
Space Group	P 1 21 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 315		2007-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.97930	NSLS	X29A

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	1.69	50	94.2	0.038	0.031	44.5	5.1	33695	33695

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)
	1.69	1.75	60		0.172	0.165	6.8	3.1	2131

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.69	23.83	33679	33679	1695	94.19	0.165	0.165	0.163	0.16	0.199	0.2	RANDOM	17.567

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]
-0.12		0.3	0.04		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.519
r_dihedral_angle_4_deg	16.898
r_dihedral_angle_3_deg	13.521
r_dihedral_angle_1_deg	4.264
r_scangle_it	3.785
r_scbond_it	2.442
r_mcangle_it	1.203
r_angle_refined_deg	1.16
r_mcbond_it	0.865
r_nbtor_refined	0.291

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.519
r_dihedral_angle_4_deg	16.898
r_dihedral_angle_3_deg	13.521
r_dihedral_angle_1_deg	4.264
r_scangle_it	3.785
r_scbond_it	2.442
r_mcangle_it	1.203
r_angle_refined_deg	1.16
r_mcbond_it	0.865
r_nbtor_refined	0.291
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.19
r_symmetry_hbond_refined	0.121
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.074
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2648
Nucleic Acid Atoms
Solvent Atoms	366
Heterogen Atoms	8

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building

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.