5TW0 | pdb_00005tw0

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		partially refined model from a different crystal form

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	20% PEG 3350, 0.2 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.576	α = 90
b = 91.576	β = 90
c = 118.705	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	2013-04-19	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	1.96	32.97	87.2	0.135	0.998	10.9	9.5		23283			30.498

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	1.96	2.01	28		0.424	0.537	1.4	1.2

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	partially refined model from a different crystal form	1.96	32.97	21941	924	85.78	0.1502	0.1484	0.16	0.1942	0.21	RANDOM	42.708

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]
1.04	0.52		1.04		-3.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.58
r_dihedral_angle_4_deg	22.796
r_dihedral_angle_3_deg	16.371
r_dihedral_angle_1_deg	7.276
r_mcangle_it	3.12
r_mcbond_other	2.288
r_mcbond_it	2.287
r_angle_refined_deg	1.12
r_angle_other_deg	0.574
r_chiral_restr	0.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.58
r_dihedral_angle_4_deg	22.796
r_dihedral_angle_3_deg	16.371
r_dihedral_angle_1_deg	7.276
r_mcangle_it	3.12
r_mcbond_other	2.288
r_mcbond_it	2.287
r_angle_refined_deg	1.12
r_angle_other_deg	0.574
r_chiral_restr	0.074
r_gen_planes_refined	0.019
r_bond_refined_d	0.008
r_gen_planes_other	0.002
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2598
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.