9AW1 | pdb_00009aw1

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

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.517	α = 90
b = 58.296	β = 90
c = 66.716	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		2023-11-02	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	1.5	24.7	99.34	0.659	9.35	10		34687

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	24.7			0.659

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	1.5	24.7	34687	1753	99.341	0.156	0.1543	0.154	0.1848	0.1859	8.844

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]
0.007			0.005		-0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.425
r_dihedral_angle_3_deg	12.166
r_dihedral_angle_2_deg	9.173
r_dihedral_angle_1_deg	7.103
r_lrange_it	5.013
r_lrange_other	4.469
r_scangle_it	2.802
r_scangle_other	2.801
r_scbond_it	1.936
r_scbond_other	1.936
r_angle_refined_deg	1.664
r_mcangle_it	1.649
r_mcangle_other	1.649
r_dihedral_angle_other_2_deg	1.29
r_mcbond_it	1.07
r_mcbond_other	1.067
r_angle_other_deg	0.586
r_nbd_refined	0.215
r_symmetry_nbd_other	0.199
r_nbd_other	0.194
r_xyhbond_nbd_refined	0.182
r_symmetry_nbd_refined	0.18
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.136
r_metal_ion_refined	0.122
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
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	342
Heterogen Atoms	16

Software

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