2OW9 | pdb_00002ow9

Crystal structure analysis of the MMP13 catalytic domain in complex with specific inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CIZ	PDB entry 1CIZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	Protein concentration: 7-20 mg/ml. Well solution: 18-22% PEG MME 5000, 0.2M Lithium sulfate, 0.1M Hepes buffer. 2-4 microliter drops with 1:1 ratio of protein complex solution and well solution, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.764	α = 90
b = 36.343	β = 93.53
c = 71.684	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	CCD	MAR CCD 165 mm	mirrors	2000-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.74	70.71	96.5	0.056	17.7	2.9		37780		2	16.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.74	1.78	67.5		0.226	1.9		2606

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1CIZ	1.74	70.71	3	37780	35279	1847	98.57	0.168	0.167	0.17	0.191	0.19	RANDOM	17.075

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]
0.43		0.18	-0.48		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.128
r_dihedral_angle_4_deg	16.726
r_dihedral_angle_3_deg	12.382
r_dihedral_angle_1_deg	5.43
r_scangle_it	1.66
r_scbond_it	1.132
r_angle_refined_deg	1.043
r_mcangle_it	0.788
r_mcbond_it	0.453
r_symmetry_metal_ion_refined	0.326
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.211
r_nbd_refined	0.181
r_symmetry_hbond_refined	0.116
r_metal_ion_refined	0.109
r_xyhbond_nbd_refined	0.105
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2651
Nucleic Acid Atoms
Solvent Atoms	418
Heterogen Atoms	82

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
AMoRE	phasing