2YQY | pdb_00002yqy

Crystal structure of TT2238, a four-helix bundle protein

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7	291	20%(w/v) PEG 1000, 100mM Tris pH 7.0, 0.2M Zn acetate, microbatch, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.846	α = 90
b = 104.846	β = 90
c = 51.254	γ = 90

Symmetry
Space Group	P 41 21 2

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	RIGAKU	A fixed exit Si double crystal monochromator followed by a two dimensional focu sing mirror which is coated in rhodium.	2005-04-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	0.97914, 0.97950, 0.90000	SPring-8	BL26B2

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	36	99.6	0.058	22.4	13.8	19790	19771

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	2.07	100		0.142	8.5	14.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2	7.98	18459	1002	99.74	0.22208	0.22032	0.26	0.25738	0.3	RANDOM	20.225

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			-0.04		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.41
r_dihedral_angle_4_deg	20.149
r_dihedral_angle_3_deg	12.717
r_dihedral_angle_1_deg	4.427
r_angle_refined_deg	1.375
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.251
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.189
r_symmetry_hbond_refined	0.164
r_chiral_restr	0.082
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1907
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms

Software

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