2I5X | pdb_00002i5x

Engineering the PTPbeta catalytic domain with improved crystallization properties

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I4H	PDB ENTRY 2I4h

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	21% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.973	α = 90
b = 71.308	β = 93.4
c = 69.69	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	MARRESEARCH	Si monochromator	2004-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

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	1.7	39.6	99.6	0.036	16.98	3.9	66068	66068			20.73

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	1.7	1.8	97.9		0.3	3.64	2.2	9811

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2I4h	1.7	39.6	66068	66068	3354	99.64	0.181	0.18	0.179	0.1777	0.207	0.206	RANDOM	22.261

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]
0.53		0.25	-0.68		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.87
r_dihedral_angle_4_deg	19.399
r_dihedral_angle_3_deg	14.985
r_dihedral_angle_1_deg	7.494
r_scangle_it	5.421
r_scbond_it	3.719
r_mcangle_it	2.557
r_mcbond_it	1.651
r_angle_refined_deg	0.92
r_nbtor_refined	0.32
r_symmetry_vdw_refined	0.301
r_symmetry_hbond_refined	0.285
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.182
r_chiral_restr	0.086
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4582
Nucleic Acid Atoms
Solvent Atoms	326
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing