1X9H | pdb_00001x9h

Crystal structure of phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum in complex with fructose 6-phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TZB	pdb entry 1TZB

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 = 55.2	α = 90
b = 100.8	β = 113.4
c = 55.9	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	1.5	36	96.8	0.063	0.063	19.5	3.6	86757	86757			16.1

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	1.5	1.55	82.8		0.391	0.391	1.7	2.8	7410

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	THROUGHOUT	pdb entry 1TZB	1.5	36	87508	86508	4290	96.38	0.153	0.153	0.152	0.16	0.18	0.19	RANDOM	16.35

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]
0.95		-0.48	-0.42		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.626
r_dihedral_angle_4_deg	17.125
r_dihedral_angle_3_deg	13.52
r_dihedral_angle_1_deg	5.124
r_sphericity_free	3.886
r_rigid_bond_restr	3.275
r_scangle_it	2.854
r_scbond_it	2.297
r_sphericity_bonded	1.466
r_angle_refined_deg	1.343
r_mcangle_it	1.192
r_angle_other_deg	1.128
r_mcbond_it	0.991
r_mcbond_other	0.268
r_symmetry_vdw_other	0.267
r_nbd_refined	0.212
r_nbd_other	0.182
r_symmetry_hbond_refined	0.182
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.144
r_symmetry_vdw_refined	0.112
r_nbtor_other	0.082
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4716
Nucleic Acid Atoms
Solvent Atoms	403
Heterogen Atoms	81

Software

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