2Q02 | pdb_00002q02

Crystal structure of a xylose isomerase domain containing protein (stm4435) from salmonella typhimurium lt2 at 2.40 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	NANODROP, 20.0% Glycerol, 0.16M Mg(OAc)2, 16.0% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.5	α = 90
b = 95.23	β = 90
c = 136.71	γ = 90

Symmetry
Space Group	P 21 21 21

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)	2007-02-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91162, 0.97922, 0.97894	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	2.4	29.386	98.5	0.057	9.83			48661		-3	44.32

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	2.4	2.49	92.4		0.322	2.4

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	2.4	29.386	48605	2435	99.3	0.186	0.184	0.19	0.228	0.23	RANDOM	44.088

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]
-1.36			-1.38		2.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.112
r_dihedral_angle_4_deg	20.184
r_dihedral_angle_3_deg	14.895
r_dihedral_angle_1_deg	5.99
r_scangle_it	4.625
r_scbond_it	3.504
r_mcangle_it	1.533
r_angle_refined_deg	1.333
r_mcbond_it	1.114
r_angle_other_deg	0.82
r_mcbond_other	0.433
r_symmetry_vdw_other	0.228
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.182
r_nbd_other	0.18
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.104
r_nbtor_other	0.084
r_chiral_restr	0.071
r_metal_ion_refined	0.07
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8552
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	27

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