9AWB | pdb_00009awb

Crystal structure of trypsin at 175 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, HANGING DROP		298	0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.441	α = 90
b = 58.303	β = 90
c = 66.74	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	175	CMOS	BRUKER PHOTON 100		2023-11-04	M	LAUE

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	1.495	23.15	98.78	0.798	12.1	10		34642

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	23.15			0.798

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	1.495	23.146	34642	1752	98.78	0.185	0.1836	0.1834	0.2182	0.2179	12.171

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]
			-0.001		0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.846
r_dihedral_angle_2_deg	12.404
r_dihedral_angle_3_deg	11.531
r_dihedral_angle_1_deg	7.156
r_lrange_it	4.837
r_lrange_other	4.48
r_scangle_it	2.943
r_scangle_other	2.942
r_scbond_it	2.066
r_scbond_other	2.065
r_mcangle_it	1.857
r_mcangle_other	1.856
r_angle_refined_deg	1.626
r_mcbond_it	1.278
r_mcbond_other	1.272
r_dihedral_angle_other_2_deg	1.241
r_angle_other_deg	0.553
r_nbd_refined	0.209
r_symmetry_nbd_other	0.196
r_symmetry_nbd_refined	0.185
r_nbd_other	0.184
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.17
r_xyhbond_nbd_refined	0.164
r_metal_ion_refined	0.117
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.079
r_gen_planes_refined	0.011
r_bond_refined_d	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	300
Heterogen Atoms	16

Software

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