1VP4 | pdb_00001vp4

Crystal structure of a putative aminotransferase (tm1131) from thermotoga maritima msb8 at 1.82 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		277	20.0% PEG-3350, 0.2M NaFormate, 2.0mM n-Dodecyl-beta-D-maltoside, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 165.125	α = 90
b = 165.125	β = 90
c = 68.701	γ = 120

Symmetry
Space Group	P 65

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		2004-08-04	M	SINGLE WAVELENGTH
2	1	x-ray		M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1		ALS	8.2.1
2	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0000,0.9796	ALS	8.2.1

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
1,2	1.82	28.41	98.2	0.054	13.8	4.8		94227			36.02

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.82	1.92	89.3		0.418	2.2	2.5	12449

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	1.82	28.41	89425	4716	98.08	0.18022	0.17902	0.19	0.20341	0.21	RANDOM	40.428

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	0.16		0.32		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.714
r_dihedral_angle_4_deg	22.09
r_dihedral_angle_3_deg	12.992
r_scangle_it	7.386
r_dihedral_angle_1_deg	6.565
r_scbond_it	5.417
r_mcangle_it	2.801
r_mcbond_it	2.226
r_angle_refined_deg	1.553
r_angle_other_deg	0.877
r_mcbond_other	0.617
r_xyhbond_nbd_other	0.242
r_symmetry_vdw_other	0.231
r_nbd_refined	0.224
r_nbd_other	0.193
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.183
r_symmetry_hbond_refined	0.16
r_symmetry_vdw_refined	0.135
r_chiral_restr	0.092
r_nbtor_other	0.089
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6535
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	148

Software

Software
Software Name	Purpose
XDSauto	data collection
SCALA	data scaling
SHELX	model building
SHARP	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling
SHELX	phasing