2PFE | pdb_00002pfe

Crystal Structure of Thermobifida fusca Protease A (TFPA)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		2.1A structure of TFPA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	8% (v/v) glycerol, 10mM MnCl2, 0.15M AmSO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.959	α = 90
b = 68.552	β = 101.98
c = 40.355	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	100	CCD	ADSC QUANTUM 315		2004-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.95	ALS	8.2.2

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	1.436	50	96.9	0.076	15.52	4	63419	61453		-3

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	1.436	1.46	87.8		0.352	2.6	2.5	2754

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	2.1A structure of TFPA	1.436	15	55164	53796	6073	97.52	0.2048	0.2048	0.20205	0.2	0.22898	0.23	RANDOM	8.462

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]
0.2		0.24	-0.21		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.133
r_dihedral_angle_4_deg	21.389
r_dihedral_angle_3_deg	10.631
r_dihedral_angle_1_deg	6.029
r_scangle_it	2.523
r_scbond_it	1.774
r_angle_refined_deg	1.329
r_mcangle_it	1.04
r_mcbond_it	0.668
r_nbtor_refined	0.303
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.195
r_symmetry_hbond_refined	0.152
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2638
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	46

Software

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