4I03 | pdb_00004i03

Human MMP12 in complex with a PEG-linked bifunctional L-glutamate motif inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Protein solution: 222 microM MMP12 mutant E219A 106 microM bifunctional inhibitor LD884. Reservoir: 27% PEG 10K, 150mM imidazole piperidine, pH 8.5. Cryoprotectant: 5 % di-ethylene glycol + 5 % ethylene glycol + 10 % 1,2-propanediol + 5 % DMSO + 5 % glycerol, 25% MPEG 5K, 100mM (Na acetate, ADA, Bicine 10% pH 4.0/90% pH 9.0), VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.79	α = 90
b = 60.1	β = 116.67
c = 54.92	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	PIXEL	PSI PILATUS 6M	mirrors	2012-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.980110	SOLEIL	PROXIMA 1

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	1.7	50	99.2	0.102	0.089	9.52	4.14	16789	16663		-4	28.35

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	1.7	1.8	97.2		0.887	0.768	1.71	4.02	2693

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	36.67	-4	16663	15828	834	100	0.14626	0.14361	0.15	0.19397	0.19	RANDOM	19.56

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]
0.05		0.06	-0.05		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.842
r_dihedral_angle_4_deg	18.651
r_dihedral_angle_3_deg	16.634
r_dihedral_angle_1_deg	7.055
r_scangle_it	4.865
r_scbond_it	3.131
r_mcangle_it	2.29
r_angle_refined_deg	2.038
r_mcbond_it	1.372
r_angle_other_deg	1.033

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.842
r_dihedral_angle_4_deg	18.651
r_dihedral_angle_3_deg	16.634
r_dihedral_angle_1_deg	7.055
r_scangle_it	4.865
r_scbond_it	3.131
r_mcangle_it	2.29
r_angle_refined_deg	2.038
r_mcbond_it	1.372
r_angle_other_deg	1.033
r_mcbond_other	0.414
r_chiral_restr	0.114
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1242
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	139

Software

Software
Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.