9AWZ | pdb_00009awz

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

X-RAY DIFFRACTION

---

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	45.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.327	α = 90
b = 57.396	β = 90
c = 67.336	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	1.488	23.12	98.56	0.684	7.124	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	23.12			0.684

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	1.488	23.078	34788	1760	98.743	0.188	0.1861	0.1958	0.2261	0.2267	18.68

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]
0.272			-0.22		-0.052

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.855
r_dihedral_angle_3_deg	13.053
r_dihedral_angle_2_deg	10.845
r_dihedral_angle_1_deg	6.516
r_lrange_it	6.136
r_lrange_other	6.128
r_scangle_it	5.204
r_scangle_other	5.204
r_scbond_it	3.404
r_scbond_other	3.402
r_mcangle_it	2.718
r_mcangle_other	2.717
r_mcbond_it	1.878
r_mcbond_other	1.875
r_angle_refined_deg	1.786
r_dihedral_angle_other_2_deg	0.778
r_angle_other_deg	0.648
r_xyhbond_nbd_refined	0.405
r_symmetry_xyhbond_nbd_refined	0.24
r_nbd_refined	0.209
r_symmetry_nbd_other	0.203
r_symmetry_nbd_refined	0.2
r_nbtor_refined	0.182
r_nbd_other	0.155
r_metal_ion_refined	0.143
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.089
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
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	80
Heterogen Atoms	10

Software

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