3KEJ

Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2. reservoir: 1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2. drop ratio: 5ul protein + 1 ul reservoir., VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.883	α = 90
b = 96.457	β = 90
c = 36.638	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	110	CCD	ADSC QUANTUM 210	crystal monochromator	2005-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

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	2.2	30	100	0.112	0.112	14.5	4.8	22451	22451	-0.5	-1	27.3

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)
	2.2	2.28	96.3		0.37	0.37	4.4	3.4	1895

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.3	29.8	18646	989	99.59	0.18602	0.1834	0.23611	RANDOM	8.15

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]
-0.75			1.09		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.673
r_dihedral_angle_4_deg	25.445
r_dihedral_angle_3_deg	13.564
r_dihedral_angle_1_deg	5.881
r_scangle_it	1.59
r_angle_refined_deg	1.153
r_scbond_it	1.092
r_angle_other_deg	0.804
r_mcangle_it	0.734
r_mcbond_it	0.428
r_nbtor_refined	0.195
r_symmetry_vdw_other	0.193
r_symmetry_hbond_refined	0.189
r_nbd_refined	0.183
r_nbd_other	0.181
r_xyhbond_nbd_refined	0.15
r_symmetry_vdw_refined	0.141
r_metal_ion_refined	0.11
r_nbtor_other	0.086
r_mcbond_other	0.08
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2531
Nucleic Acid Atoms
Solvent Atoms	400
Heterogen Atoms	74

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling