3P6L | pdb_00003p6l

Crystal structure of a Sugar phosphate isomerase/epimerase (BDI_1903) from Parabacteroides distasonis ATCC 8503 at 1.85 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.33	277	45.5% polyethylene glycol 600, 0.1M phosphate-citrate pH 4.33, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.382	α = 90
b = 73.014	β = 103.73
c = 47.536	γ = 90

Symmetry
Space Group	C 1 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	ADSC QUANTUM 315		2010-09-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9537,0.9796,0.9794	ALS	8.2.2

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	1.85	28.638	99.6	0.09	7.9	3	23324	23324			22.447

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	1.85	1.9	100		0.818	0.818	0.8	3	1756

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	1.85	28.638	23228	1197	99.17	0.1889	0.1862	0.19	0.2385	0.24	RANDOM	27.5871

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]
-1.33		-2.4	-0.95		1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.347
r_dihedral_angle_4_deg	14.707
r_dihedral_angle_3_deg	13.898
r_scangle_it	5.767
r_dihedral_angle_1_deg	4.917
r_scbond_it	4.088
r_mcangle_it	2.339
r_angle_refined_deg	1.599
r_mcbond_it	1.373
r_angle_other_deg	0.926

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.347
r_dihedral_angle_4_deg	14.707
r_dihedral_angle_3_deg	13.898
r_scangle_it	5.767
r_dihedral_angle_1_deg	4.917
r_scbond_it	4.088
r_mcangle_it	2.339
r_angle_refined_deg	1.599
r_mcbond_it	1.373
r_angle_other_deg	0.926
r_mcbond_other	0.302
r_chiral_restr	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2112
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	32

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
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.