3GIW | pdb_00003giw

CRYSTAL STRUCTURE OF a DUF574 family protein (SAV_2177) FROM STREPTOMYCES AVERMITILIS MA-4680 AT 1.45 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	1.0 M Na citrate, 0.1 M Sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.716	α = 90
b = 49.669	β = 94.72
c = 45.132	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	Flat collimating mirror, toroid focusing mirror	2009-01-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837, 0.97927	SSRL	BL9-2

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	1.45	27.186	94.8	0.036	13.4	4.063		50240		-3	15.987

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	1.45	1.5	85.9		0.333	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.45	27.186	50239	2551	98.99	0.157	0.156	0.16	0.176	0.18	RANDOM	18.557

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]
-0.35		-0.42	-0.8		1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.735
r_dihedral_angle_4_deg	14.108
r_dihedral_angle_3_deg	11.96
r_dihedral_angle_1_deg	5.86
r_scangle_it	2.498
r_mcangle_it	1.815
r_scbond_it	1.719
r_angle_refined_deg	1.511
r_mcbond_it	1.249
r_angle_other_deg	1.003
r_mcbond_other	0.307
r_symmetry_vdw_other	0.286
r_nbd_refined	0.219
r_nbd_other	0.203
r_symmetry_hbond_refined	0.198
r_nbtor_refined	0.174
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.169
r_xyhbond_nbd_other	0.102
r_chiral_restr	0.099
r_nbtor_other	0.081
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2023
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing