3A4T | pdb_00003a4t

Crystal structure of aTrm4 from M.jannaschii with sinefungin

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A1X	PDB ENTRY 3A1X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	100mM Tris-HCl buffer (pH 7.4) , 200mM MgCl2 ,25% PEG 3350, 10mM cytidine, 3mM sinefungin, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.259	α = 90
b = 40.097	β = 110.84
c = 85.951	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	ADSC QUANTUM 315		2008-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.00	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.3	42.45	1	0.022	0.024	19.5	3.6		24668

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.38	100		0.564	0.627	0.488	2.04	2457

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 (All)	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 3A1X	2.3	42.45	23355	23309	1248	99.78	0.18551	0.18551	0.18116	0.1813	0.26756	0.2676	RANDOM	22.653

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.5
r_dihedral_angle_4_deg	21.199
r_dihedral_angle_3_deg	20.052
r_dihedral_angle_1_deg	8.712
r_scangle_it	5.029
r_scbond_it	3.386
r_angle_refined_deg	2.284
r_mcangle_it	1.843
r_mcbond_it	1.163
r_symmetry_hbond_refined	0.357
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.241
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.178
r_chiral_restr	0.154
r_bond_refined_d	0.027
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4111
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	54

Software

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