2GB3 | pdb_00002gb3

Crystal structure of Aspartate aminotransferase (tm1698) from Thermotoga maritima at 2.50 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XI9	pdb entry 1xi9A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	4.5	277	35.0% 2-propanol, 0.1M Acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.094	α = 90
b = 214.051	β = 112.31
c = 76.839	γ = 90

Symmetry
Space Group	P 1 21 1

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 315	Flat mirror (vertical focusing)	2005-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	2.496	107.211	97.5	0.139	0.139	3.4	3.4		75747

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)
1	2.5	2.56	89.4		0.2	0.2	3.5	1.9

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	pdb entry 1xi9A	2.5	107.03	75283	3781	97.52	0.231	0.229	0.24	0.266	0.27	RANDOM	28.427

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]
-3.1		1.06	1.78		2.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.265
r_dihedral_angle_3_deg	8.558
r_dihedral_angle_4_deg	8.21
r_scangle_it	2.472
r_scbond_it	1.731
r_dihedral_angle_1_deg	1.537
r_angle_refined_deg	1.526
r_angle_other_deg	0.927
r_mcangle_it	0.629
r_mcbond_it	0.508
r_symmetry_hbond_refined	0.263
r_nbd_refined	0.189
r_nbtor_refined	0.177
r_symmetry_vdw_other	0.175
r_xyhbond_nbd_refined	0.169
r_mcbond_other	0.167
r_symmetry_vdw_refined	0.155
r_nbd_other	0.153
r_chiral_restr	0.091
r_nbtor_other	0.085
r_symmetry_hbond_other	0.07
r_xyhbond_nbd_other	0.03
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18179
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing