2I22 | pdb_00002i22

Crystal structure of Escherichia coli phosphoheptose isomerase in complex with reaction substrate sedoheptulose 7-phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TK9	PDB entry 1TK9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	298	3% PEG 8000, 0.002 M DTT, 3% 1,6-hexanediol, 0.01 M Hepes, 0.1 M imidazole, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.045	α = 90
b = 76.54	β = 106.13
c = 78.316	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	IMAGE PLATE	RIGAKU RAXIS IV		2005-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.79	47.39	98.6			20533	20533	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.79	2.89	99.4

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 1TK9	2.8	25	18807	18807	1478	100	0.20694	0.20297	0.19	0.25699	0.24	RANDOM	44.337

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]
0.21		-0.51	-0.34		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.003
r_dihedral_angle_4_deg	24.483
r_dihedral_angle_3_deg	20.234
r_dihedral_angle_1_deg	6.752
r_scangle_it	5.438
r_scbond_it	3.83
r_mcangle_it	2.853
r_angle_refined_deg	2.845
r_mcbond_it	2.039
r_nbtor_refined	0.35
r_nbd_refined	0.301
r_symmetry_vdw_refined	0.243
r_xyhbond_nbd_refined	0.221
r_chiral_restr	0.187
r_symmetry_hbond_refined	0.178
r_bond_refined_d	0.038
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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	5436
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
CNS	phasing