9AWR | pdb_00009awr

Crystal structure of trypsin at 275 Kelvin with benzamidine (duplicate)

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
2.22	44.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.258	α = 90
b = 57.015	β = 90
c = 66.971	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	275	PIXEL	Bruker PHOTON II		2023-11-08	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	1.491	25.157	98.58	0.743	1.57	10		34045

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	25.14			0.743

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	1.491	25.157	34045	1687	98.521	0.24	0.2392	0.244	0.2641	0.2685	12.081

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]
-0.398			0.421		-0.024

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.764
r_dihedral_angle_3_deg	12.721
r_dihedral_angle_2_deg	11.221
r_dihedral_angle_1_deg	7.535
r_lrange_it	5.197
r_lrange_other	4.928
r_scangle_it	3.221
r_scangle_other	3.22
r_mcangle_it	2.42
r_mcangle_other	2.42
r_scbond_it	2.072
r_scbond_other	2.071
r_angle_refined_deg	1.619
r_mcbond_it	1.448
r_mcbond_other	1.447
r_dihedral_angle_other_2_deg	1.106
r_angle_other_deg	0.58
r_xyhbond_nbd_refined	0.408
r_nbd_refined	0.208
r_symmetry_nbd_other	0.201
r_nbd_other	0.187
r_nbtor_refined	0.173
r_metal_ion_refined	0.161
r_symmetry_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.134
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.08
r_symmetry_metal_ion_refined	0.069
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
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	129
Heterogen Atoms	10

Software

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