3NMN | pdb_00003nmn

Crystal structure of pyrabactin-bound abscisic acid receptor PYL1 in complex with type 2C protein phosphatase ABI1

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.2M ammonium sulphate, 0.1M BisTris, 22% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.978	α = 115.78
b = 66.71	β = 95.43
c = 72.598	γ = 105.6

Symmetry
Space Group	P 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	MARMOSAIC 300 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.00	APS	21-ID-D

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	2.15	30	92	0.098	49.1	13.4	50236	46283	2	2

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 (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 3KDJ	2.15	29.62	50236	46283	3617	96.99	0.21301	0.2103	0.22	0.24751	0.25	RANDOM	40.935

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]
0.28	-1.47	-2.38	0.11	1.22	-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.28
r_dihedral_angle_4_deg	20.253
r_dihedral_angle_3_deg	15.062
r_sphericity_free	14.877
r_sphericity_bonded	5.583
r_scangle_it	5.425
r_dihedral_angle_1_deg	4.677
r_scbond_it	3.638
r_mcangle_it	3.306
r_rigid_bond_restr	2.702
r_mcbond_it	1.869
r_angle_refined_deg	1.552
r_angle_other_deg	0.909
r_mcbond_other	0.771
r_chiral_restr	0.092
r_bond_refined_d	0.02
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6956
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	48

Software

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