9AWM | pdb_00009awm

Crystal structure of trypsin at 225 Kelvin with benzamidine (Triplicate)

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
2.2	44.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.866	α = 90
b = 57.041	β = 90
c = 66.72	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	225	CMOS	BRUKER PHOTON 100		2023-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER TURBO X-RAY SOURCE	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	1.499	23.59	93.81	0.808	7.51	10		33354

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	23.58			0.808

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	1.499	23.59	33354	1652	99.073	0.193	0.1911	0.1912	0.2186	0.2188	13.447

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]
-0.036			0.089		-0.053

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	14.692
r_dihedral_angle_6_deg	14.397
r_dihedral_angle_3_deg	11.589
r_dihedral_angle_1_deg	6.717
r_lrange_it	5.664
r_lrange_other	5.421
r_scangle_it	3.671
r_scangle_other	3.671
r_scbond_it	2.379
r_scbond_other	2.377
r_mcangle_it	2.371
r_mcangle_other	2.37
r_angle_refined_deg	1.718
r_mcbond_it	1.491
r_mcbond_other	1.489
r_dihedral_angle_other_2_deg	1.011
r_angle_other_deg	0.608
r_xyhbond_nbd_refined	0.323
r_symmetry_xyhbond_nbd_refined	0.248
r_nbd_refined	0.22
r_symmetry_nbd_other	0.204
r_nbd_other	0.18
r_nbtor_refined	0.175
r_symmetry_nbd_refined	0.162
r_metal_ion_refined	0.127
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.032
r_bond_refined_d	0.009
r_gen_planes_refined	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	193
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SCALA	data scaling
MOLREP	phasing