2Q03 | pdb_00002q03

Crystal structure of uncharacterized protein (YP_563039.1) from Shewanella denitrificans OS217 at 1.80 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.61	277	NANODROP, 15.9% Ethanol, 0.2M Magnesium chloride, 0.1M HEPES pH 7.61, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4	69.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.83	α = 90
b = 145.83	β = 90
c = 45.47	γ = 90

Symmetry
Space Group	P 41 21 2

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)	2007-04-29	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97926, 0.97904	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	1.8	29.161	99.8	0.059	11.64	7.2		46034		-3	29.12

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	1.8	1.86	99.2		0.466	2.53

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	1.8	29.161	45976	2322	99.85	0.168	0.167	0.18	0.183	0.19	RANDOM	31.343

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		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.989
r_dihedral_angle_4_deg	13.671
r_dihedral_angle_3_deg	11.245
r_scangle_it	8.185
r_scbond_it	5.539
r_dihedral_angle_1_deg	4.986
r_mcangle_it	3.303
r_mcbond_it	2.321
r_angle_refined_deg	1.783
r_angle_other_deg	0.851
r_mcbond_other	0.507
r_symmetry_hbond_refined	0.259
r_xyhbond_nbd_refined	0.212
r_nbtor_refined	0.18
r_nbd_other	0.172
r_nbd_refined	0.168
r_symmetry_vdw_other	0.15
r_symmetry_vdw_refined	0.106
r_chiral_restr	0.105
r_nbtor_other	0.088
r_bond_refined_d	0.018
r_symmetry_hbond_other	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2008
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	12

Software

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