6FJ2 | pdb_00006fj2

Structure of Thermolysin solved from SAD data collected at the peak of the Zn absorption edge on ID30B

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	0.05M MES, 1M NaCl, 45% DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.717	α = 90
b = 92.717	β = 90
c = 128.621	γ = 120

Symmetry
Space Group	P 61 2 2

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 PILATUS3 6M		2017-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	1.282	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	80.3	96.7	0.079	0.096	0.042	0.99	13.6	2.8		60230			11.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.43	1.45	79.1		0.203	0.262	0.137	0.93	3.7	2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.43	80.3	57172	3000	98.68	0.14523	0.14425	0.15	0.16405	0.17	RANDOM	16.417

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]
-0.07	-0.04		-0.07		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.359
r_dihedral_angle_4_deg	15.475
r_dihedral_angle_3_deg	12.1
r_dihedral_angle_1_deg	5.591
r_long_range_B_refined	4.381
r_long_range_B_other	4.175
r_scangle_other	2.327
r_scbond_it	2.036
r_scbond_other	2.035
r_angle_refined_deg	1.71
r_mcangle_it	1.342
r_mcangle_other	1.342
r_mcbond_it	1.066
r_angle_other_deg	1.044
r_mcbond_other	1.039
r_chiral_restr	0.109
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2449
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing