3NMP | pdb_00003nmp

Crystal structure of the abscisic receptor PYL2 mutant A93F in complex with pyrabactin

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.1	293	2M ammonium acetate, 22% PEG 3350, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.084	α = 90
b = 105.571	β = 90
c = 182.901	γ = 90

Symmetry
Space Group	C 2 2 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	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	2.1	30	87	0.093	27.6	8.2		32811	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 3NMH	2.1	29.39	35374	30793	2526	99.72	0.23583	0.23355	0.24	0.26634	0.27	RANDOM	45.552

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]
0.04			0.06		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.029
r_dihedral_angle_4_deg	18.542
r_sphericity_free	15.256
r_dihedral_angle_3_deg	14.063
r_sphericity_bonded	8.575
r_scangle_it	5.139
r_dihedral_angle_1_deg	4.382
r_mcangle_it	3.791
r_scbond_it	3.631
r_rigid_bond_restr	3.553
r_mcbond_it	2.212
r_angle_refined_deg	1.555
r_mcbond_other	1.187
r_angle_other_deg	0.907
r_chiral_restr	0.102
r_bond_refined_d	0.02
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4203
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	66

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling