3TSK | pdb_00003tsk

Human MMP12 in complex with L-glutamate motif inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TS4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	293	MMP-12 at 0.4 mM co-crystallized with 100 mM AHA and compound QEG at 1 mM against reservoir solution: 27% PEG 10000, 100 mM Tris-HCl, pH 9.5. 24h in cryoprotectant to remove AHA. 70 MICRO-M compound QEG in 10% di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10K, 200 mM NaCl, 33.3 mM sodium acetate, 33.3 mM ADA, 33.3 mM bicine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.71	α = 90
b = 63.06	β = 90
c = 37.95	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MARMOSAIC 225 mm CCD	bent cylindrical mirror	2011-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2	33.33	83.9	0.142	0.074	7.2	3.7		9572

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	80.9		1.066	0.926	1.6	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	RIGID BODY REFINEMENT	THROUGHOUT	3TS4	2	33.331	11288	9114	458	80.74	0.1655	0.16216	0.16	0.23174	0.23	RANDOM	27.721

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]
-1.44			-0.26		1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.632
r_dihedral_angle_3_deg	14.952
r_dihedral_angle_4_deg	10.712
r_dihedral_angle_1_deg	6.596
r_scangle_it	4.129
r_scbond_it	2.7
r_angle_refined_deg	2.22
r_mcangle_it	1.756
r_mcbond_it	1.017
r_chiral_restr	0.177
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1246
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	45

Software

Software
Software Name	Purpose
DNA	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing