5K2Z | pdb_00005k2z

PDX1.3-adduct (Arabidopsis)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NV2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	50 mM MES.OH pH 6.5, 0.7 M ammonium sulfate, 5% 1,4-dioxane, 10 mM Tris.HCl pH 6.5, 0.1 M potassium chloride, and 5 mM dithiothreitol.

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.46	α = 90
b = 178.46	β = 90
c = 115.81	γ = 120

Symmetry
Space Group	H 3

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 EIGER X 16M		2015-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.97858	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.761	92.68	99.5	0.087	9.9	5.7		135507

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	1.761	1.86	99.2		0.882	0.8	5.2

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	2NV2	1.8	92.68	120693	6292	99.59	0.1814	0.1803	0.1894	0.2036	0.188	RANDOM	31.446

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]
-1.64	-0.82		-1.64		5.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.941
r_dihedral_angle_4_deg	17.419
r_dihedral_angle_3_deg	13.026
r_dihedral_angle_1_deg	5.676
r_mcangle_it	4.107
r_mcbond_other	3.154
r_mcbond_it	3.153
r_angle_refined_deg	1.427
r_angle_other_deg	1.167
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8302
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms	86

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing