5L7F | pdb_00005l7f

Crystal structure of MMP12 mutant K421A in complex with RXP470.1 conjugated with fluorophore Cy5,5 in space group P21.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CZM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	293	protein: MMP12-F171D-K241A 661 micro-M + 10 milli-M AHA, 10% DMSO, 0.5 milli-M fluorescent inhibitor (R47-CY5) precipitant: 20% PEG4K, 2% gamma valerolactone, 0.2 milli-M TRIS pH 9.5 40% CM26 ((12.5 % diethylene glycol + 12.5 % ethylene glycol + 12.5 % glycerol + 25 % 2,3-butanediol + 12.5 % DMSO), 25% MPEG 6K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.92	α = 90
b = 70.37	β = 104.61
c = 52.22	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M	mirrors	2015-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.978570	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	CC (Half)	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	1.79	47.34	96.9	0.145	0.113	0.988	6.87	2.386860603		63601		-3

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	1.79	1.84	98.4		0.947	1.43	2.36172043

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 (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	5CZM	1.8	47.34	30250	1593	99.33	0.17656	0.1756	0.19	0.19464	0.2	RANDOM	21.924

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]
1.01		-1.96	-1.52		1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.784
r_dihedral_angle_4_deg	18.917
r_dihedral_angle_3_deg	12.698
r_long_range_B_refined	8.466
r_long_range_B_other	8.214
r_dihedral_angle_1_deg	6.42
r_scangle_other	5.036
r_scbond_it	3.823
r_scbond_other	3.821
r_mcangle_it	3.015
r_mcangle_other	3.014
r_angle_other_deg	2.529
r_mcbond_it	2.091
r_mcbond_other	2.085
r_angle_refined_deg	1.8
r_chiral_restr	0.111
r_gen_planes_other	0.024
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.009
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2468
Nucleic Acid Atoms
Solvent Atoms	364
Heterogen Atoms	283

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building