1X7N | pdb_00001x7n

The crystal structure of Pyrococcus furiosus phosphoglucose isomerase with bound 5-phospho-D-arabinonate and Manganese

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	1.6M tri-sodium citrate, 50mM 5-phospho-D-arabinonate, 100mM MnCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.674	α = 90
b = 42.382	β = 120.57
c = 57.255	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	IMAGE PLATE	MARRESEARCH	yale mirrors	2003-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54

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	49.39	97.9	0.052	4.5	3	13726	13726

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	81.3		0.349	2.79	2.3	741

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 (All)	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	1PLZ	1.89	49.39	13075	651	96.97	0.1439	0.1439	0.14051	0.15	0.21226	0.15	RANDOM	30.619

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]
-0.13		-0.19	0.26		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	31.869
r_scangle_it	28.127
r_mcangle_it	14.296
r_mcbond_it	12.569
r_dihedral_angle_1_deg	7.053
r_angle_refined_deg	1.354
r_angle_other_deg	0.739
r_symmetry_vdw_other	0.269
r_nbd_other	0.239
r_nbd_refined	0.201
r_symmetry_hbond_refined	0.145
r_xyhbond_nbd_refined	0.135
r_symmetry_vdw_refined	0.133
r_chiral_restr	0.082
r_nbtor_other	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1519
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing