5TXW

Structure of Pfp1 protease from Thermococcus thioreducens: large cell H3 crystal form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G2I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	1.4 M Sodium Citrate, pH 6.5, vapor diffusion, sitting drop

Crystal Properties
Matthews coefficient	Solvent content
2.528	51.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.85	α = 90
b = 152.85	β = 90
c = 82.541	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	RIGAKU SATURN 944+	Osmic mirrors	2013-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54187

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.86	38.22	86.3	0.123	0.992	11.9	8.8		52126			15.88

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.9	33.5		0.583	0.485	0.6	1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1G2I	1.86	38.22	49624	2499	86.27	0.12962	0.1274	0.1734	RANDOM	20.02

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]
-0.11	-0.06		-0.11		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.176
r_dihedral_angle_4_deg	21.643
r_dihedral_angle_3_deg	15.169
r_long_range_B_refined	11.307
r_long_range_B_other	11.17
r_scangle_other	8.535
r_dihedral_angle_1_deg	7.896
r_scbond_it	5.693
r_scbond_other	5.691
r_mcangle_it	3.675
r_mcangle_other	3.675
r_mcbond_it	2.718
r_mcbond_other	2.707
r_angle_refined_deg	1.23
r_angle_other_deg	0.628
r_chiral_restr	0.078
r_gen_planes_refined	0.02
r_bond_refined_d	0.009
r_gen_planes_other	0.002
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5196
Nucleic Acid Atoms
Solvent Atoms	639
Heterogen Atoms

Software

Software
Software Name	Purpose
iMOSFLM	data reduction
Aimless	data scaling
CNS	phasing
REFMAC	refinement
Coot	model building