4EFS | pdb_00004efs

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	3LIK	PDB entry 3LIK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Protein solution - 0.53 mM F67D mutant of human MMP12 residues 106-263 in 0.1 M acetohydroxamic acid 0.003 M CaCl2, 0.200 M NaCl 0.02 M Tris-HCl, pH 7.5. Reservoir solution -27% PEG 10K,0.2 M imidazole malate cryoconditions - CryoProtX-Cryomix 7, 25% MPEG 5K, 0.1 M AAB 10/90, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.97	α = 90
b = 63.19	β = 90
c = 37.51	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	PIXEL	PSI PILATUS 6M	mirrors	2012-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.918400	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	1.63	46.59	97.4	0.086	0.083	18.72	8.72	21260	20710			25.023

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	1.63	1.72	99.3		0.726	0.683	3.31	8.55	3230

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	RIGID BODY	THROUGHOUT	PDB entry 3LIK	1.63	46.59	-3	21260	20063	1056	100	0.15554	0.15368	0.15	0.19044	0.19	RANDOM	20.811

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]
-1.05			-0.31		1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.385
r_dihedral_angle_4_deg	21.192
r_dihedral_angle_3_deg	14.826
r_dihedral_angle_1_deg	6.638
r_scangle_it	5.809
r_scbond_it	3.74
r_mcangle_it	2.682
r_angle_refined_deg	2.607
r_mcbond_it	1.613
r_chiral_restr	0.182
r_bond_refined_d	0.029
r_gen_planes_refined	0.016
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	139
Heterogen Atoms	73

Software

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