4Z9B | pdb_00004z9b

Crystal structure of Low Molecular Weight Protein Tyrosine Phosphatase isoform A complexed with benzylphosphonic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5PNT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	32% (w/v) PEG 5000, 0.1 M malic acid:Tris, molar ratio 1:2, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.088	α = 90
b = 54.287	β = 90
c = 97.468	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	APEX II CCD		2013-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	2.4	27.8	99.7	0.1455	16.34	11.84		7097

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	2.4	2.45	100		0.5618	2.94	11.58

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	5PNT	2.41	27.8	6641	325	99.26	0.21875	0.21479	0.22	0.30148	0.3	RANDOM	35.003

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]
1.77			-1.7		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.456
r_dihedral_angle_4_deg	20.462
r_dihedral_angle_3_deg	15.492
r_dihedral_angle_1_deg	6.825
r_long_range_B_refined	4.635
r_long_range_B_other	4.634
r_mcangle_it	2.513
r_mcangle_other	2.512
r_scangle_other	2.334
r_angle_refined_deg	1.562
r_mcbond_it	1.502
r_mcbond_other	1.502
r_scbond_it	1.393
r_scbond_other	1.393
r_angle_other_deg	0.89
r_chiral_restr	0.077
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1249
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	11

Software

Software
Software Name	Purpose
APEX	data collection
APEX	data reduction
APEX	data scaling
PHASER	phasing
REFMAC	refinement