3A7X | pdb_00003a7x

Crystal Structure of Trypsin complexed with (E)-2-(4-carbamimidoylbenzylideneaminooxy)acetic acid (soaking 45seconds)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A7T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.1M Tris-HCl, 30% PEG 3350, 0.2M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.717	α = 90
b = 56.887	β = 90
c = 66.057	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	IMAGE PLATE	RIGAKU RAXIS VII			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.75	50	99.9	0.034	0.034	39.8	5.6				-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.75	1.81	98.9		0.092	0.092	11.7	4

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	3A7T	1.75	19.57	19853	1055	99.72	0.15774	0.15643	0.16	0.18329	0.15	RANDOM	15.356

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]
-0.12			-0.01		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.085
r_dihedral_angle_4_deg	18.096
r_dihedral_angle_3_deg	10.821
r_dihedral_angle_1_deg	6.095
r_scangle_it	3.088
r_scbond_it	1.946
r_angle_refined_deg	1.26
r_mcangle_it	1.201
r_mcbond_it	0.726
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.085
r_dihedral_angle_4_deg	18.096
r_dihedral_angle_3_deg	10.821
r_dihedral_angle_1_deg	6.095
r_scangle_it	3.088
r_scbond_it	1.946
r_angle_refined_deg	1.26
r_mcangle_it	1.201
r_mcbond_it	0.726
r_nbtor_refined	0.298
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.178
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.132
r_metal_ion_refined	0.122
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1629
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	35

Software

Software
Software Name	Purpose
LAFIRE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
LAFIRE	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.