3HYI | pdb_00003hyi

Crystal structure of full-length DUF199/WhiA from Thermatoga maritima

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	0.1 M Tris, pH 8.0, 0.2 M NaCl, 10% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.648	α = 90
b = 61.303	β = 90
c = 97.215	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	IMAGE PLATE	R-AXIS IV++	mirrors	2009-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	2.34	50	98.6	0.053	27	4.7	13590	13400

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	2.34	2.42	98.3		0.347	5	4.6	1294

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	N-terminal "LAGLIDADG" domain of T. maritima DUF199/WhiA	2.34	35.4	12702	666	98.69	0.23014	0.22775	0.23	0.27608	0.28	RANDOM	20.876

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]
-0.46			-0.17		0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.638
r_dihedral_angle_4_deg	16.323
r_dihedral_angle_3_deg	14.767
r_dihedral_angle_1_deg	5.933
r_angle_refined_deg	0.868
r_scangle_it	0.796
r_angle_other_deg	0.767
r_scbond_it	0.466
r_mcangle_it	0.358
r_symmetry_vdw_other	0.241
r_symmetry_vdw_refined	0.206
r_mcbond_it	0.192
r_nbd_refined	0.186
r_nbd_other	0.175
r_nbtor_refined	0.172
r_symmetry_hbond_refined	0.129
r_xyhbond_nbd_refined	0.114
r_nbtor_other	0.086
r_chiral_restr	0.05
r_mcbond_other	0.025
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2175
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	13

Software

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