4WU2 | pdb_00004wu2

Structure of the PTP-like myo-inositol phosphatase from Selenomonas ruminantium in complex with myo-inositol-(1,4,5)-trikisphosphate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.8	293	PEG 8000, sodium acetate, sodium chloride, beta-mercapto ethanol

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.98	α = 90
b = 137.67	β = 102.42
c = 80.01	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	RAYONIX MX-300		2011-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	.97934	CLSI	08ID-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	44.9	99.9	0.128	5.2	3.3		65377

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	2.15	2.22	100		0.523	1.9	3.3

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	3MMJ	2.15	44.89	50511	2154	99.86	0.19768	0.19677	0.19	0.21947	0.21	RANDOM	31.039

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]
-2.59		0.48	-0.82		2.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.71
r_dihedral_angle_4_deg	18.685
r_dihedral_angle_3_deg	13.2
r_long_range_B_refined	9.339
r_long_range_B_other	9.326
r_scangle_other	6.292
r_dihedral_angle_1_deg	5.192
r_mcangle_other	4.501
r_mcangle_it	4.5
r_scbond_it	4.112
r_scbond_other	4.112
r_mcbond_it	3.027
r_mcbond_other	3.023
r_angle_refined_deg	1.153
r_angle_other_deg	0.62
r_chiral_restr	0.059
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d
r_gen_planes_other
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5096
Nucleic Acid Atoms
Solvent Atoms	484
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling