9AWU | pdb_00009awu

Crystal structure of trypsin at 300 Kelvin with benzamidine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S0R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.4	298	0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.333	α = 90
b = 57.39	β = 90
c = 67.409	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	300	PIXEL	Bruker PHOTON II		2023-11-08	M	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER X8 PROTEUM	1.54184

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.482	23.071	97.42	0.716	7.82	10		34783

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	23.07			0.716

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.482	23.071	34783	1754	97.423	0.204	0.2022	0.2121	0.2397	0.2452	18.287

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]
0.006			-0.01		0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.735
r_dihedral_angle_3_deg	12.877
r_dihedral_angle_2_deg	11.22
r_dihedral_angle_1_deg	6.643
r_lrange_it	5.696
r_lrange_other	5.603
r_scangle_it	4.595
r_scangle_other	4.595
r_scbond_it	3.002
r_scbond_other	3.001
r_mcangle_it	2.58
r_mcangle_other	2.579
r_mcbond_it	1.753
r_mcbond_other	1.751
r_angle_refined_deg	1.584
r_dihedral_angle_other_2_deg	0.709
r_angle_other_deg	0.552
r_xyhbond_nbd_refined	0.394
r_symmetry_nbd_refined	0.304
r_nbd_other	0.303
r_nbd_refined	0.218
r_symmetry_nbd_other	0.2
r_symmetry_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.181
r_metal_ion_refined	0.125
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_other	0.037
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1629
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
MOLREP	phasing