1HUK | pdb_00001huk

REFINED STRUCTURE OF YEAST INORGANIC PYROPHOSPHATASE AND ITS K61R MUTANT

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PYP	LOW RESOLUTION STRUCTURE (PDB ENTRY 1PYP)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microliter drops	6.5	277	CRYSTALLIZATION CONDITIONS: 10 MG/ML PROTEIN IN 0.1 M MES (PH 6.5) BUFFER. 10 MICROLITER DROPS IN 9 WELL DEPRESSION PLATE IN A PLASTIC SANDWICH BOX CONTAINING 15 MILLILITER OF 0.1 M MES(PH 6.5) + 16 % MPD. EVERY ALTERNATE DAY, MPD CONCENTRATION INCREASED BY 1 % UNTIL FINAL CONCENTRATION REACHED 25 %. 4 DEGREE C. WITHIN 15 DAYS, 0.2 X 0.3 X 0.4 MM CRYSTALS., microliter drops, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.6	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.09	α = 90
b = 93.06	β = 99.62
c = 51.58	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	93	IMAGE PLATE	RIGAKU RAXIS	MSC/YALE MIRRORS	1995-03-25	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.23	30	91.7	0.044		2.7		28288			14.1

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	LOW RESOLUTION STRUCTURE (PDB ENTRY 1PYP)	2.2	8	27238	2704	85.1	0.193	0.193	0.18	0.288	0.27	RANDOM	15.5

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	26.5
x_scangle_it	5.1
x_scbond_it	3.62
x_mcangle_it	3.14
x_mcbond_it	2.18
x_improper_angle_d	2
x_angle_deg	1.1
x_bond_d	0.009
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4492
Nucleic Acid Atoms
Solvent Atoms	311
Heterogen Atoms	2

Software

Software
Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
X-PLOR	phasing