3ODP | pdb_00003odp

Crystal structure of a putative tagatose-6-phosphate ketose/aldose isomerase (NT01CX_0292) from CLOSTRIDIUM NOVYI NT at 2.35 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I0Z	PDB entry 3I0Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	50.00% PEG-200, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.364	α = 90
b = 89.364	β = 90
c = 120.012	γ = 120

Symmetry
Space Group	P 32 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 mirror (vertical focusing)	2008-08-06	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.35	77.391	100	0.084	12.7	7.4	23656	23656			57.921

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	2.35	2.48	100		0.01	1.042	0.7	7.5	3398

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	SAD + MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3I0Z	2.35	77.391	23616	1215	99.97	0.2297	0.2278	0.23	0.264	0.26	RANDOM	89.0472

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]
0.47	0.23		0.47		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.604
r_dihedral_angle_4_deg	17.223
r_dihedral_angle_3_deg	16.179
r_dihedral_angle_1_deg	5.867
r_scangle_it	1.745
r_angle_refined_deg	1.175
r_scbond_it	1.121
r_angle_other_deg	0.859
r_mcangle_it	0.608
r_mcbond_it	0.329

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.604
r_dihedral_angle_4_deg	17.223
r_dihedral_angle_3_deg	16.179
r_dihedral_angle_1_deg	5.867
r_scangle_it	1.745
r_angle_refined_deg	1.175
r_scbond_it	1.121
r_angle_other_deg	0.859
r_mcangle_it	0.608
r_mcbond_it	0.329
r_mcbond_other	0.074
r_chiral_restr	0.066
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3022
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	25

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
SHELXD	phasing
autoSHARP	phasing
MOLREP	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.