1Y25

structure of mycobacterial thiol peroxidase Tpx

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.089	α = 90
b = 106.089	β = 90
c = 65.334	γ = 120

Symmetry
Space Group	P 31 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	100	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2004-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	2.1	92.06	99.4	0.048	0.048	19.7	3.5	24893	24893			31.673

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	2.1	2.21	98.5		0.26	0.26	3.7	2.8	3567

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1psq	2.1	30.77	23364	23364	1274	98.23	0.17461	0.17461	0.17076	0.2493	RANDOM	25.707

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]
-0.1	-0.05		-0.1		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.82
r_dihedral_angle_4_deg	25.774
r_dihedral_angle_3_deg	15.749
r_dihedral_angle_1_deg	7.262
r_scangle_it	3.975
r_scbond_it	2.853
r_angle_refined_deg	2.32
r_mcangle_it	1.696
r_mcbond_it	1.386
r_angle_other_deg	1.011
r_symmetry_vdw_refined	0.328
r_mcbond_other	0.306
r_symmetry_vdw_other	0.303
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.21
r_nbd_other	0.203
r_symmetry_hbond_refined	0.199
r_nbtor_refined	0.176
r_chiral_restr	0.121
r_nbtor_other	0.09
r_bond_refined_d	0.024
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2378
Nucleic Acid Atoms
Solvent Atoms	368
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing