2AJR | pdb_00002ajr

Crystal structure of Possible 1-phosphofructokinase (EC 2.7.1.56) (tm0828) from Thermotoga Maritima at 2.46 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	293	16% PEG-8000, 0.08M sodium cacodylate, 0.16M magnesium acetate tetrahydrate, 20% glyerol anhyrous , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.94	57.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.796	α = 90
b = 115.796	β = 90
c = 124.828	γ = 90

Symmetry
Space Group	P 41 21 2

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	ADSC QUANTUM 315	FLAT MIRROR	2002-06-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.885567,0.976224	SSRL	BL11-1

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	2.4	29.2	99.5	0.109	0.109	5.9	6.3		31322

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	2.46	2.52	95		0.633	0.633	1.2	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.46	28.49	29692	1595	99.4	0.193	0.1966	0.24	0.2413	RANDOM	31.77

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]
1.31			1.31		-2.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.829
r_dihedral_angle_3_deg	17.005
r_dihedral_angle_4_deg	15.688
r_scangle_it	6.864
r_dihedral_angle_1_deg	6.194
r_scbond_it	5.131
r_mcangle_it	2.525
r_mcbond_it	1.719
r_angle_refined_deg	1.274
r_angle_other_deg	0.825
r_mcbond_other	0.391
r_nbd_refined	0.204
r_symmetry_vdw_other	0.204
r_nbd_other	0.183
r_nbtor_refined	0.181
r_symmetry_hbond_refined	0.159
r_symmetry_vdw_refined	0.158
r_xyhbond_nbd_refined	0.148
r_nbtor_other	0.086
r_chiral_restr	0.073
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5013
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SnB	phasing
MLPHARE	phasing
SOLVE	phasing