4HGC | pdb_00004hgc

Crystal structure of bovine trypsin complexed with sfti-1 analog containing a peptoid residue at position p1

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	292	2.3 M ammonium sulphate, 1 mM benzamidine and 0.1 M Mes, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.12	α = 90
b = 64.14	β = 90
c = 70.04	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	100	CCD	MAR CCD 165 mm	mirrors	2007-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8148	EMBL/DESY, HAMBURG	X11

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	1.29	37.17	99.4	0.057	16.5	7.2	67689	67689		-3	19.74

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	1.29	1.36	98.6		0.804	2	6.8	9680

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 (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	R-free	PDB ENTRY 1SFI	1.29	30.74	65592	65592	2036	99.2	0.12714	0.12623	0.13	0.1567	0.16	RANDOM	16.878

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]
-0.1					0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.014
r_sphericity_free	29.371
r_dihedral_angle_4_deg	19.989
r_sphericity_bonded	14.591
r_dihedral_angle_3_deg	10.617
r_dihedral_angle_1_deg	6.738
r_rigid_bond_restr	4.977
r_angle_other_deg	2.098
r_angle_refined_deg	1.978
r_chiral_restr	0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.014
r_sphericity_free	29.371
r_dihedral_angle_4_deg	19.989
r_sphericity_bonded	14.591
r_dihedral_angle_3_deg	10.617
r_dihedral_angle_1_deg	6.738
r_rigid_bond_restr	4.977
r_angle_other_deg	2.098
r_angle_refined_deg	1.978
r_chiral_restr	0.13
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.007
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1719
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	46

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.