4LUM | pdb_00004lum

The crystal structure of the P132V mutant of Pyrococcus furiosus phosphoglucose isomerase in complex with manganese and fructose-6- phosphate.

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, SITTING DROP	6.5	290	0.2 M sodium nitrate, 0.1 M Bis Tris Propane PH6.5, 20% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.94	α = 87.81
b = 45.01	β = 89.86
c = 48.69	γ = 75.47

Symmetry
Space Group	P 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 I03	2011-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96860	Diamond	I24

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	1.79	18.49	95.7	0.086	4.3	1.8	33074	33074

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	1.79	1.84	94		0.349	2.2	1.8	2386

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	1.79	18.49	33074	31398	1675	100	0.17577	0.17325	0.17	0.22008	0.22	RANDOM	27.347

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]
0.83	1.08	0.42	-0.37	-0.37	-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.881
r_dihedral_angle_4_deg	16.549
r_dihedral_angle_3_deg	14.214
r_dihedral_angle_1_deg	6.421
r_scangle_it	4.352
r_scbond_it	2.621
r_mcangle_it	1.851
r_angle_refined_deg	1.265
r_rigid_bond_restr	1.242
r_mcbond_it	0.997

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.881
r_dihedral_angle_4_deg	16.549
r_dihedral_angle_3_deg	14.214
r_dihedral_angle_1_deg	6.421
r_scangle_it	4.352
r_scbond_it	2.621
r_mcangle_it	1.851
r_angle_refined_deg	1.265
r_rigid_bond_restr	1.242
r_mcbond_it	0.997
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3056
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	34

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.