3TT4 | pdb_00003tt4

Human MMP8 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	2OY2	PDB ENTRY 2OY2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	MMP-8 at 400 micro-M co-crystallization with peptidic inhibitor with reservoir solution 17.5% PEG 20K, 0.1 M MES, 0.125 M NACL. VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K. Inhibitor exchange: 24hr soak in 25% PEG 4K instead of 17.5% PEG20K with 100 micro-M E1S inhibitor in 6 micro-L volume cryoprotectant is 12% PEG10K, 13.75% MPEG2K, 5% di-ethylene glycol, 10% 1,2-propanediol, 10% glycerol, 0.025 M MES PH 5.5, 30 sec cryoprotectant soak

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.719	α = 90
b = 69.369	β = 90
c = 70.312	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	100	CCD	ADSC QUANTUM 315r	bent cylindrical mirror	2011-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97242	ESRF	ID23-1

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	1.88	60	98.1	0.247	0.222	8.9	5.26	13650	13397		-3	24.39

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	1.88	2.01	99.6		1.026	0.919	2.08	5.2	12439

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 (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 2OY2	1.88	34.69	12970	12729	667	98.14	0.19409	0.19087	0.2	0.2578	0.27	RANDOM	21.835

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]
-1.73			-1.79		3.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.691
r_dihedral_angle_4_deg	21.05
r_dihedral_angle_3_deg	16.025
r_dihedral_angle_1_deg	7.547
r_scangle_it	4.249
r_scbond_it	3.103
r_mcangle_it	2.071
r_angle_refined_deg	2.012
r_mcbond_it	1.278
r_chiral_restr	0.24
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
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	1253
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	42

Software

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