9PCT | pdb_00009pct

Structure of Porcine Trypsin Crystals Grown from PEG Complexed with Crystallization Additives III

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	Sitting drop vapor diffusion in Cryschem plates with 0.6 ml reservoirs of 30% PEG 3350 buffered at pH 6.5 with 0.1 M HEPES. Drops 3 ul of reservoir, 2 ul of additive mix ( TACSIMATE, glycerol, sucrose, sorbitol), 3 ul of 40 mg/ml stock protein solution buffered at pH 6.5 with 0.1 M HEPES.

Crystal Properties
Matthews coefficient	Solvent content
2.2	48.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.82	α = 90
b = 58.82	β = 90
c = 135.34	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	IMAGE PLATE	RIGAKU	Osmic mirrors	2012-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	1.41	27.1	78.7	0.053	13.5	3.41		36756			18.65

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	1.41	1.46			0.27	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.41	26.31	1	36297	2547	77.88	0.134	0.1312	0.1313	0.1698	0.17	43.32

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.3632
f_angle_d	1.3317
f_chiral_restr	0.0962
f_bond_d	0.0078
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1642
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	379

Software

Software
Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
Aimless	data scaling
PHASER	phasing