3DRW | pdb_00003drw

Crystal Structure of a Phosphofructokinase from Pyrococcus horikoshii OT3 with AMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U2X	1U2X molecule A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20% PEG 3350, 0.2 M Lithium Citrate plus 5 mM ADP Cryoprotected in N-paratone oil., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.464	α = 90
b = 104.19	β = 105.09
c = 70.844	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	ADSC QUANTUM 315	mirrors	2007-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97929	APS	19-ID

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	1.9	50	98.7	0.08	16.7	4.5	75838	74815			23.5

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	1.9	1.97	90.7		0.353	3.2	3.9	6856

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1U2X molecule A	1.9	41.45	74775	71005	3770	98.27	0.17426	0.17161	0.18	0.2244	RANDOM	29.37

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]
-0.05		0.03	0.1		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.107
r_dihedral_angle_4_deg	18.377
r_dihedral_angle_3_deg	15.637
r_dihedral_angle_1_deg	7.542
r_scangle_it	5.917
r_scbond_it	3.545
r_mcangle_it	1.991
r_angle_refined_deg	1.8
r_mcbond_it	1.082
r_nbtor_refined	0.316
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.215
r_chiral_restr	0.165
r_symmetry_hbond_refined	0.153
r_xyhbond_nbd_refined	0.15
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
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	7379
Nucleic Acid Atoms
Solvent Atoms	576
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing