2E2D

Flexibility and variability of TIMP binding: X-ray structure of the complex between collagenase-3/MMP-13 and TIMP-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	830C	PDB ENTRY 830C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	100 mM MES, 200 mM magnesium acetate, 20 % PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
3.55	65.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.526	α = 90
b = 72.526	β = 90
c = 181.375	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	Mirrors	1999-01-29	M	SINGLE WAVELENGTH
2	1	100	IMAGE PLATE	MAR scanner 345 mm plate	Mirrors	1999-04-26

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418
2	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.0503	MPG/DESY, HAMBURG	BW6

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	23.77	0.999	0.06	0.06	25.1	8.6	36318	36318			30.492

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	2.07	0.999		0.498	0.498	0.031	4.5	3606

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 830C	2	23.77	34445	34445	1800	100	0.20144	0.20144	0.19991	0.2313	RANDOM	30.492

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]
1.48	0.74		1.48		-2.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.653
r_dihedral_angle_1_deg	4.698
r_scangle_it	3.484
r_scbond_it	2.187
r_mcangle_it	1.653
r_angle_refined_deg	1.626
r_mcbond_it	0.898
r_angle_other_deg	0.795
r_symmetry_vdw_other	0.428
r_symmetry_vdw_refined	0.392
r_metal_ion_refined	0.376
r_nbd_refined	0.278
r_xyhbond_nbd_refined	0.256
r_nbd_other	0.222
r_xyhbond_nbd_other	0.177
r_symmetry_hbond_refined	0.171
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_other
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	2725
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DNA	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling