5MOQ | pdb_00005moq

Joint X-ray/neutron structure of cationic trypsin in complex with benzamidine

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4I8H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, 13.0-16.5% (w/v) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.901	α = 90
b = 58.614	β = 90
c = 67.604	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	PIXEL	DECTRIS PILATUS 6M		2015-06-10	M	SINGLE WAVELENGTH
2	1	neutron	295	IMAGE PLATE	MAATEL BIODIFF		2014-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.7749	PETRA III, EMBL c/o DESY	P14 (MX2)
2	NUCLEAR REACTOR	FRM II BEAMLINE BIODIFF	2.673	FRM II	BIODIFF

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	0.93	42.618	99.5	0.039						28.68	8.633		145727
2	1.5	50	89.4	0.071						10.197	2.4		31713

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.93	0.99		0.565						4.47	8.435
2	1.5	1.53		0.267						3.244	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	0.93	27.451		1.35		145639	7330	99.51		0.0963	0.0959	0.1	0.1032	0.1	Random selection
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.502	25.434				31693	1573	89.42		0.1512	0.1504		0.1667		Random selection

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	15.404
f_dihedral_angle_d	15.404
f_angle_d	1.189
f_angle_d	1.189
f_chiral_restr	0.098
f_chiral_restr	0.098
f_plane_restr	0.008
f_plane_restr	0.008
f_bond_d	0.006
f_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1609
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	15

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
HKL-2000	data reduction
XDS	data scaling
HKL-2000	data scaling
PHASER	phasing

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.