5N5J

Human MMP12 in complex with 3-(5-(1,2-dithiolan-3-yl)pentanamido)propane-1-sulfonate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y93

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.1 M Tris-HCl, 20% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.926	α = 90
b = 60.47	β = 114.55
c = 53.844	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	OXFORD ONYX CCD		2015-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION ENHANCE ULTRA	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.8	24.49	93.4	0.076	0.031	5.6	6.2		12916			8.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	77.4		0.175	0.175	3.1	1.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1Y93	1.8	24.29	12255	660	93.34	0.12909	0.12545	0.19533	RANDOM	15.609

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]
-0.48		-0.02	0.04		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.341
r_sphericity_free	19.178
r_dihedral_angle_3_deg	11.105
r_sphericity_bonded	10.549
r_rigid_bond_restr	8.034
r_dihedral_angle_1_deg	6.584
r_dihedral_angle_4_deg	6.014
r_scangle_other	4.71
r_scbond_it	4.296
r_scbond_other	3.994
r_long_range_B_refined	3.919
r_long_range_B_other	3.852
r_mcangle_other	2.48
r_mcangle_it	2.468
r_mcbond_it	2.303
r_mcbond_other	2.284
r_angle_refined_deg	1.979
r_angle_other_deg	1.148
r_chiral_restr	0.13
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1238
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	29

Software

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