2Q9P | pdb_00002q9p

Human diphosphoinositol polyphosphate phosphohydrolase 1, Mg-F complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FVV	PDB entry 2FVV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	30% PEG 8000, 200 mM LiCl, 5 mM MgCl2, 20 mM NaF, 5 mM IP6, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.193	α = 90
b = 59.444	β = 90
c = 62.547	γ = 90

Symmetry
Space Group	P 21 21 21

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	Bruker Platinum 135	Helios multilayer mirrors	2007-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR

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	1.65	50	99.8	0.054	11.7	2.1	20890	20848		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.65	1.75	99.3		0.461	2.1

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 (All)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 2FVV	1.65	32.21	20848	20813	1067	99.7	0.194	0.194	0.192	0.2	0.23	0.23	RANDOM	15.789

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]
0.02			-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.112
r_dihedral_angle_4_deg	20.631
r_dihedral_angle_3_deg	13.81
r_dihedral_angle_1_deg	6.861
r_scangle_it	4.469
r_scbond_it	3.211
r_angle_refined_deg	1.846
r_mcangle_it	1.761
r_mcbond_it	1.591
r_angle_other_deg	1.001
r_mcbond_other	0.357
r_nbd_other	0.215
r_nbd_refined	0.212
r_metal_ion_refined	0.188
r_xyhbond_nbd_refined	0.183
r_symmetry_vdw_other	0.18
r_nbtor_refined	0.173
r_symmetry_hbond_refined	0.157
r_chiral_restr	0.122
r_nbtor_other	0.094
r_symmetry_vdw_refined	0.084
r_xyhbond_nbd_other	0.027
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1110
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	87

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	data reduction
SADABS	data scaling
REFMAC	phasing