3VPY | pdb_00003vpy

Crystal structure of Arabidopsis DDL FHA domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PEG, HEPES, AS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.564	α = 90
b = 48.709	β = 90
c = 54.688	γ = 90

Symmetry
Space Group	P 21 21 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	ADSC QUANTUM 315r		2009-03-06	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9792	SSRF	BL17U

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	36.37	99.84	0.064		7.6	13290	13269	2	2

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	1.73	100		0.521	4.3	7.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.7	36.37	13290	13269	1487	99.84	0.19204	0.18769	0.1846	0.23107	0.2281	RANDOM	22.617

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]
0.32			-0.54		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.727
r_dihedral_angle_4_deg	14.691
r_dihedral_angle_3_deg	13.579
r_dihedral_angle_1_deg	6.472
r_scangle_it	4.016
r_scbond_it	2.562
r_mcangle_it	1.369
r_angle_refined_deg	1.285
r_mcbond_it	0.85
r_nbtor_refined	0.301
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.18
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.109
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1162
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms

Software

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