1TZC | pdb_00001tzc

Crystal structure of phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum in complex with 5-phosphoarabinonate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		NATIVE STRUCTURE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	25% polyethylene glycol 8000, 0.22M ammonium sulphate, 100mM Tris, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.1	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.8	α = 90
b = 100.85	β = 113.7
c = 55.8	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD		2003-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.45	36	97.8	0.078	0.078	13.4	2.9	97954	97954			17.1

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	1.45	1.5	94.3		0.462	0.462	1.6	2.5	9407

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 (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	REFINEMENT FROM NATIVE STRUCTURE	THROUGHOUT	NATIVE STRUCTURE	1.45	36	97736	97736	4866	94.2	0.17	0.17	0.169	0.18	0.192	0.2	RANDOM	15.34

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]
-0.37		-0.26	-0.04		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.827
r_scangle_it	3.147
r_scbond_it	1.829
r_angle_refined_deg	1.273
r_mcangle_it	1.099
r_angle_other_deg	1.091
r_mcbond_it	0.586
r_symmetry_vdw_other	0.257
r_nbd_other	0.233
r_nbd_refined	0.209
r_symmetry_hbond_refined	0.144
r_xyhbond_nbd_refined	0.13
r_symmetry_vdw_refined	0.104
r_nbtor_other	0.081
r_chiral_restr	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4717
Nucleic Acid Atoms
Solvent Atoms	439
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling