4LUK | pdb_00004luk

The crystal structure of the P132A, Y133G mutant of Pyrococcus furiosus phosphoglucose isomerase in complex with manganese and 5-phospho-D-arabinonate.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X7N	PDB ENTRY 1X7N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	290	0.35 M MgCl2, 0.1 M sodium acetate PH 5.5 and 19% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.85	α = 90
b = 43.28	β = 122.9
c = 58.45	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	PIXEL	DECTRIS PILATUS 6M	Diamond IO3	2011-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97630	Diamond	I03

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	1.41	28.92	91.2	0.036	13	3.1	32797	32797

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	1.41	1.44	55.4		0.349	2.1	2.4	1460

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1X7N	1.41	28.92	32797	31134	1663	100	0.15336	0.15009	0.16	0.21388	0.21	RANDOM	26.299

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]
-1.79		-1.83	2.35		-2.56

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	86.29
r_scangle_it	78.163
r_rigid_bond_restr	52.302
r_mcbond_it	37.221
r_mcangle_it	35.504
r_dihedral_angle_2_deg	29.068
r_mcbond_other	21.17
r_dihedral_angle_4_deg	12.722
r_dihedral_angle_3_deg	10.587
r_dihedral_angle_1_deg	5.954

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	86.29
r_scangle_it	78.163
r_rigid_bond_restr	52.302
r_mcbond_it	37.221
r_mcangle_it	35.504
r_dihedral_angle_2_deg	29.068
r_mcbond_other	21.17
r_dihedral_angle_4_deg	12.722
r_dihedral_angle_3_deg	10.587
r_dihedral_angle_1_deg	5.954
r_angle_refined_deg	1.064
r_angle_other_deg	0.726
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1510
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	32

Software

Software
Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
xia2	data reduction
xia2	data scaling

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.