5A7I | pdb_00005a7i

Crystal structure of INPP5B in complex with biphenyl 3,3',4,4',5,5'- hexakisphosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N9V	PDB ENTRY 3N9V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.2		10% GLYCEROL, 25% PROPANEDIOL AND 0.1 M SODIUM/POTASSIUM PHOSPHATE PH 6.2

Crystal Properties
Matthews coefficient	Solvent content
4.96	75.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.975	α = 90
b = 96.975	β = 90
c = 152.142	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	MARMOSAIC 225 mm CCD	MIRRORS	2011-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1		BESSY	14.1

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	2.89	34.29	99.9	0.07	21.2	7		16922		-3

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	2.89	3.05	100		0.84	2.2	7.2

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	PDB ENTRY 3N9V	2.89	34.29	16012	858	99.87	0.19826	0.197	0.19	0.22324	0.22	RANDOM	71.185

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]
-1.25			-1.25		2.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.76
r_dihedral_angle_4_deg	16.177
r_dihedral_angle_3_deg	14.137
r_dihedral_angle_1_deg	5.705
r_angle_refined_deg	1.191
r_scangle_it	1.132
r_angle_other_deg	0.771
r_scbond_it	0.641
r_mcangle_it	0.456
r_mcbond_it	0.237
r_chiral_restr	0.064
r_mcbond_other	0.03
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2545
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing