4LUL | pdb_00004lul

The crystal structure of the P132A, Y133D mutant of Pyrococcus furiosus phosphoglucose isomerase in complex with manganese.

X-RAY DIFFRACTION

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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 calcium acetate, 0.1 M sodium acetate PH6.5, 40% PEG300., VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.3	α = 90
b = 60.03	β = 90
c = 146.67	γ = 90

Symmetry
Space Group	P 21 21 21

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	1.89	25.85	98.5	0.028	15.9	3.5	29381	29381

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	1.89	1.94	99.2		0.352	2.4	3.5	2144

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	1.89	25.58	39381	27836	1489	100	0.19871	0.19588	0.1952	0.25341	0.2538	RANDOM	33.754

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]
1.21			-0.4		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.365
r_dihedral_angle_4_deg	16.746
r_dihedral_angle_3_deg	14.531
r_dihedral_angle_1_deg	6.389
r_scangle_it	4.151
r_scbond_it	2.595
r_mcangle_it	1.99
r_rigid_bond_restr	1.373
r_angle_refined_deg	1.327
r_mcbond_it	1.112
r_chiral_restr	0.092
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3028
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	2

Software

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