2IK7 | pdb_00002ik7

Yeast inorganic pyrophosphatase variant D120N with magnesium and phosphate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	277	16% MPD, 10 MM MGCL2, 1 MM PO4-, VAPOR DIFFUSION, TEMPERATURE 277K, pH 6.00

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.652	α = 90
b = 93	β = 99.33
c = 69.266	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	MULTILAYER	2002-01-08	M	SINGLE WAVELENGTH

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

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	1.9	100	99.3	0.091	0.091	7.7	3.5		50505

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)
	1.9	1.94	96.6		0.542	0.542	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	1HUK	1.9	4.48	44163	2370	100	0.1568	0.15398	0.17	0.20986	0.22	RANDOM	23.835

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]
		-0.01	-0.03		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.859
r_scangle_it	3.392
r_scbond_it	2.227
r_angle_refined_deg	1.503
r_mcangle_it	1.287
r_angle_other_deg	0.864
r_mcbond_it	0.748
r_symmetry_vdw_other	0.366
r_symmetry_vdw_refined	0.332
r_symmetry_hbond_refined	0.254
r_nbd_other	0.252
r_nbd_refined	0.24
r_xyhbond_nbd_refined	0.21
r_metal_ion_refined	0.104
r_chiral_restr	0.091
r_nbtor_other	0.084
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	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_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	4428
Nucleic Acid Atoms
Solvent Atoms	736
Heterogen Atoms	13

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling