6SWV | pdb_00006swv

Trypsin fast data collection

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ATI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	15 mg/ml protein, 100 mM benzamidine, 25% PEG 8000, 0.2 M ammonium sulfate, 100 mM Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.28	α = 90
b = 57.944	β = 90
c = 66.947	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	100	PIXEL	DECTRIS EIGER X 4M		2018-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	1.43	50	99.1	0.1	0.043	0.998	11.6	5.3		39193

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.43	1.48	97.2		1.719	0.751	0.43	0.9	4.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	3ATI	1.432	43.812	39129	1897	98.936	0.186	0.185	0.18	0.2058	0.2	11.097

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]
0.017			0.006		-0.024

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.51
r_dihedral_angle_4_deg	20.792
r_dihedral_angle_3_deg	11.524
r_dihedral_angle_1_deg	7.195
r_lrange_it	3.792
r_lrange_other	3.663
r_scangle_it	3.078
r_scangle_other	3.078
r_scbond_it	2.223
r_scbond_other	2.222
r_dihedral_angle_other_2_deg	2.156
r_angle_refined_deg	1.784
r_angle_other_deg	1.614
r_mcangle_it	1.511
r_mcangle_other	1.511
r_mcbond_it	1.022
r_mcbond_other	1.022
r_symmetry_nbd_refined	0.238
r_nbd_refined	0.196
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.161
r_nbd_other	0.144
r_metal_ion_refined	0.122
r_xyhbond_nbd_refined	0.109
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	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	232
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing