9AWV | pdb_00009awv

Crystal structure of trypsin at 300 Kelvin with benzamidine (duplicate)

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
2.22	44.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.214	α = 90
b = 57.413	β = 90
c = 66.567	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		2023-11-09	M	SINGLE WAVELENGTH

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	1.483	25.443	95.1	0.743	8.8	10		34788

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	25.41			0.743

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	1.484	25.443	33339	1680	95.067	0.218	0.2164	0.2244	0.2446	0.2494	22.881

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]
-0.943			0.009		0.934

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.097
r_dihedral_angle_6_deg	12.787
r_dihedral_angle_1_deg	7.201
r_lrange_it	6.194
r_lrange_other	6.142
r_dihedral_angle_2_deg	5.96
r_scangle_it	4.888
r_scangle_other	4.888
r_scbond_it	3.232
r_scbond_other	3.23
r_mcangle_it	3.091
r_mcangle_other	3.09
r_mcbond_it	2.074
r_mcbond_other	2.074
r_angle_refined_deg	1.638
r_angle_other_deg	0.587
r_xyhbond_nbd_refined	0.382
r_dihedral_angle_other_2_deg	0.312
r_symmetry_nbd_refined	0.259
r_nbd_refined	0.208
r_symmetry_nbd_other	0.206
r_symmetry_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.176
r_metal_ion_refined	0.162
r_nbd_other	0.16
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.085
r_symmetry_xyhbond_nbd_other	0.022
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
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