2Q9K | pdb_00002q9k

Crystal structure of a putative oxidoreductase (exig_1997) from exiguobacterium sibiricum 255-15 at 1.59 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	NANODROP, 0.17M Sodium acetate, 25.5% PEG 4000, 15.0% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.314	α = 90
b = 56.314	β = 90
c = 95.205	γ = 120

Symmetry
Space Group	P 31 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	2007-06-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162, 0.97908	SSRL	BL9-2

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	1.59	26.997	100	0.067	0.067	5.9	7.1		24172			24.182

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	1.59	1.63	100		0.832	0.832	0.9	6.7	1753

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	1.59	26.997	24135	1232	99.96	0.206	0.203	0.21	0.252	0.25	RANDOM	19.654

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]
0.27	0.13		0.27		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.651
r_dihedral_angle_4_deg	20.551
r_dihedral_angle_3_deg	15.594
r_dihedral_angle_1_deg	6.149
r_scangle_it	3.598
r_scbond_it	2.546
r_mcangle_it	1.836
r_angle_refined_deg	1.654
r_mcbond_it	1.294
r_angle_other_deg	0.961
r_mcbond_other	0.315
r_symmetry_vdw_other	0.272
r_symmetry_vdw_refined	0.258
r_nbd_refined	0.245
r_nbd_other	0.204
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.172
r_symmetry_hbond_refined	0.112
r_chiral_restr	0.111
r_nbtor_other	0.091
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1160
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	11

Software

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