9GRG | pdb_00009grg

StmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine serine protease in complex with PMSF

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Solved with the model 9G8V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293.15	0.9 M Ammonium sulfate 0.4 M Lithium sulfate 0.1 M Sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.902	α = 90
b = 85.747	β = 90
c = 130.747	γ = 90

Symmetry
Space Group	C 2 2 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 PILATUS 6M-F		2019-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

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	1.89	49.154	99.7	0.113	0.121	0.045	0.999	11.6	7.2		54075

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	1.89	2.03	99.7		0.412	0.446	0.169	0.96	4.9	6.9

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.89	49.154	27330	1062	99.843	0.177	0.1747	0.1778	0.2354	0.2362	RANDOM	28.394

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]
-1.718			3.997		-2.279

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.591
r_dihedral_angle_6_deg	13.357
r_dihedral_angle_1_deg	7.04
r_lrange_it	5.97
r_dihedral_angle_2_deg	5.69
r_scangle_it	4.636
r_scbond_it	3.44
r_mcangle_it	3.231
r_mcbond_it	2.417
r_angle_refined_deg	1.718
r_nbtor_refined	0.31
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.189
r_metal_ion_refined	0.155
r_symmetry_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.115
r_chiral_restr	0.111
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2528
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	55

Software

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