2FM1 | pdb_00002fm1

Crystal structure of L-ALLO-threonine aldolase (tm1744) from Thermotoga maritima at 2.25 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JG8	PDB entry 1jg8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	7.5	277	0.19M CaCl2, 5.0% Glycerol, 26.6% PEG-400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.21	43.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.614	α = 90
b = 100.405	β = 90
c = 149.648	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	CCD	APS-1	sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2004-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

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	2.25	150	97	0.11		7.3		67017

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	2.25	2.3		71.4	0.554		2.6

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 (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 1jg8	2.25	83.33	63488	3400	96.9	0.146	0.146	0.142	0.16	0.216	0.22	RANDOM	23.99

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]
-0.3			0.94		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.43
r_dihedral_angle_4_deg	14.767
r_dihedral_angle_3_deg	13.516
r_scangle_it	6.976
r_dihedral_angle_1_deg	6.404
r_scbond_it	4.676
r_mcangle_it	2.53
r_angle_refined_deg	1.58
r_mcbond_it	1.539
r_angle_other_deg	0.897
r_mcbond_other	0.642
r_symmetry_vdw_other	0.211
r_nbd_refined	0.189
r_nbd_other	0.185
r_symmetry_hbond_refined	0.179
r_symmetry_vdw_refined	0.167
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.164
r_metal_ion_refined	0.148
r_chiral_restr	0.088
r_nbtor_other	0.086
r_symmetry_metal_ion_refined	0.085
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10508
Nucleic Acid Atoms
Solvent Atoms	1059
Heterogen Atoms	19

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
HKL-2000	data scaling
REFMAC	refinement