9AW4 | pdb_00009aw4

Crystal structure of trypsin at 125 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, HANGING DROP	9.4	298	0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.49	α = 90
b = 58.282	β = 90
c = 66.66	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	125	CMOS	BRUKER PHOTON 100		2023-11-01	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	23.989	98.87	0.813	19.03	10		34353

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	23.97			0.813

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	23.989	34353	1708	98.869	0.192	0.1902	0.1986	0.2197	0.23	7.611

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]
-0.073			0.062		0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.968
r_dihedral_angle_2_deg	11.655
r_dihedral_angle_3_deg	11.555
r_dihedral_angle_1_deg	7.153
r_lrange_it	4.632
r_lrange_other	4.012
r_scangle_it	2.248
r_scangle_other	2.248
r_angle_refined_deg	1.703
r_dihedral_angle_other_2_deg	1.59
r_scbond_it	1.438
r_scbond_other	1.437
r_mcangle_it	1.31
r_mcangle_other	1.31
r_mcbond_it	0.812
r_mcbond_other	0.808
r_angle_other_deg	0.613
r_xyhbond_nbd_refined	0.276
r_nbd_refined	0.218
r_symmetry_xyhbond_nbd_refined	0.205
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.178
r_symmetry_nbd_refined	0.167
r_nbd_other	0.163
r_metal_ion_refined	0.141
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.084
r_symmetry_metal_ion_refined	0.025
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	309
Heterogen Atoms	10

Software

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