3FXA | pdb_00003fxa

Crystal structure of a putative sugar-phosphate isomerase (lmof2365_0531) from listeria monocytogenes str. 4b f2365 at 1.60 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.9	277	NANODROP, 0.2M Mg formate, 20.0% PEG 3350, No Buffer pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP	6.3	277	NANODROP, 0.2M NH4Cl, 20.0% PEG 3350, No Buffer pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.944	α = 90
b = 57.944	β = 90
c = 197.964	γ = 120

Symmetry
Space Group	P 31

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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2008-10-11	M	MAD
2	2	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2008-10-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.94645	APS	23-ID-B
2	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97966, 0.94645	APS	23-ID-B

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
1,2	1.6	28.976	99.6	0.085	0.085	5.726	4.7		97660			20.164

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)
1,2	1.6	1.64	97.2		0.652	0.652	1.8	3.3	7053

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 + MOLECULAR REPLACEMENT	THROUGHOUT	1.6	28.976	97613	4850	99.5	0.135	0.133	0.14	0.157	0.14	RANDOM + TWIN LAW	18.562

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]
4.62			4.62		-9.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.651
r_dihedral_angle_4_deg	15.858
r_dihedral_angle_3_deg	10.881
r_scangle_it	4.574
r_dihedral_angle_1_deg	3.473
r_scbond_it	3.229
r_mcangle_it	1.822
r_angle_refined_deg	1.605
r_angle_other_deg	1.339
r_mcbond_it	1.154

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.651
r_dihedral_angle_4_deg	15.858
r_dihedral_angle_3_deg	10.881
r_scangle_it	4.574
r_dihedral_angle_1_deg	3.473
r_scbond_it	3.229
r_mcangle_it	1.822
r_angle_refined_deg	1.605
r_angle_other_deg	1.339
r_mcbond_it	1.154
r_mcbond_other	0.267
r_chiral_restr	0.094
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5695
Nucleic Acid Atoms
Solvent Atoms	443
Heterogen Atoms	8

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.