2OQM | pdb_00002oqm

Crystal structure of a dinb family member protein (sden_0562) from shewanella denitrificans at 1.83 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	NANODROP, 0.271M Ammonium formate, 18.5% Polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.437	α = 90
b = 71.722	β = 107.35
c = 93.489	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-01-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97908, 0.97874	SSRL	BL11-1

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	1.83	45.22	92.9	0.065	8.61			68483			31.626

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	1.83	1.9	83.2		0.467	2.2		6155

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 (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	MAD	THROUGHOUT	1.83	45.22	68463	3437	98.4	0.159	0.159	0.157	0.16	0.196	0.2	RANDOM	24.558

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]
-0.79		-2.01	-0.3		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.015
r_dihedral_angle_4_deg	21.231
r_dihedral_angle_3_deg	13.141
r_scangle_it	6.534
r_dihedral_angle_1_deg	4.867
r_scbond_it	4.857
r_mcangle_it	2.761
r_mcbond_it	2.002
r_angle_refined_deg	1.492
r_angle_other_deg	1.089
r_mcbond_other	0.84
r_symmetry_vdw_other	0.279
r_symmetry_vdw_refined	0.256
r_nbd_refined	0.227
r_nbtor_refined	0.192
r_nbd_other	0.188
r_xyhbond_nbd_refined	0.171
r_symmetry_hbond_refined	0.166
r_chiral_restr	0.094
r_nbtor_other	0.091
r_bond_refined_d	0.018
r_bond_other_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5581
Nucleic Acid Atoms
Solvent Atoms	545
Heterogen Atoms	141

Software

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