4QKZ

X-ray structure of the catalytic domain of MMP-8 with the inhibitor ML115

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	10 % PEG 6000, 0.2M MES/NAOH, 1M NA PHOSPHATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.91	α = 90
b = 68.69	β = 90
c = 70.69	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		PIXEL	PSI PILATUS 6M		2013-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.2	49.26	99.17	0.09	10.2		45495	45495			12.98

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.3	99.2		0.456	2.52		10641

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3DPE	1.2	49.26	45495	5056	99.17	0.17197	0.17197	0.16952	0.1937	RANDOM	9.976

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]
0.25			0.23		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.967
r_sphericity_free	22.661
r_dihedral_angle_4_deg	18.927
r_dihedral_angle_3_deg	11.074
r_sphericity_bonded	8.611
r_dihedral_angle_1_deg	6.996
r_rigid_bond_restr	2.739
r_long_range_B_refined	1.976
r_long_range_B_other	1.733
r_angle_refined_deg	1.522
r_scangle_other	1.209
r_scbond_it	0.959
r_scbond_other	0.959
r_angle_other_deg	0.881
r_mcangle_it	0.839
r_mcangle_other	0.838
r_mcbond_it	0.808
r_mcbond_other	0.801
r_chiral_restr	0.135
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	1282
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	41

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling