6KRX

Crystal Structure of AtPTP1 at 1.7 angstrom

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	0.1 M sodium citrate (pH 6.0), 25 ~ 30% polyethylene glycol (PEG) 3350, 0.2 M potassium iodide.

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.536	α = 90
b = 38.97	β = 110.815
c = 75.525	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS PILATUS 6M		2016-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.978	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	50	96.6	0.043	0.049	0.021	0.994	30.4	4.8		34099

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	78.4		0.191	0.22	0.106	0.951	6	4

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2HNP	1.7	37.201	34081	1713	96.465	0.152	0.1511	0.1743	Random selection	16.394

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]
0.138		0.088	-0.251		0.035

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.11
r_dihedral_angle_4_deg	13.933
r_dihedral_angle_3_deg	11.811
r_lrange_it	6.357
r_lrange_other	6.271
r_dihedral_angle_1_deg	6.105
r_scangle_it	5.041
r_scangle_other	5.04
r_mcangle_other	3.556
r_mcangle_it	3.554
r_scbond_it	3.292
r_scbond_other	3.29
r_mcbond_it	2.334
r_mcbond_other	2.328
r_angle_refined_deg	1.279
r_angle_other_deg	0.339
r_nbd_refined	0.211
r_nbtor_refined	0.167
r_nbd_other	0.166
r_symmetry_nbd_other	0.163
r_symmetry_xyhbond_nbd_refined	0.154
r_xyhbond_nbd_refined	0.149
r_symmetry_nbd_refined	0.136
r_symmetry_xyhbond_nbd_other	0.107
r_symmetry_nbtor_other	0.091
r_xyhbond_nbd_other	0.087
r_chiral_restr	0.057
r_gen_planes_refined	0.056
r_gen_planes_other	0.052
r_bond_refined_d	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2391
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing