8K4Z

Crystal structure of human MMP-7 in complex with inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y6C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	20% w/v Polyethylene glycol 3350, 100mM Bis-Tris propane pH7.5, 200mM Sodium iodide

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.799	α = 90
b = 75.799	β = 90
c = 60.53	γ = 90

Symmetry
Space Group	I 4

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 PILATUS3 6M		2018-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00003	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	53.6	99.9	0.992	7.9	11.9		18920

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79			0.54

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	53.598	18916	913	99.915	0.205	0.203	0.22	0.2392	0.25	18.838

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]
-1.469			-1.469		2.939

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.937
r_dihedral_angle_4_deg	23.558
r_dihedral_angle_3_deg	13.236
r_dihedral_angle_1_deg	7.892
r_lrange_it	5.948
r_lrange_other	5.937
r_scangle_other	3.141
r_scangle_it	3.14
r_mcangle_it	2.47
r_mcangle_other	2.468
r_scbond_other	1.888
r_scbond_it	1.886
r_angle_refined_deg	1.555
r_mcbond_it	1.52
r_mcbond_other	1.52
r_angle_other_deg	1.352
r_nbd_refined	0.207
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.167
r_nbd_other	0.157
r_symmetry_xyhbond_nbd_refined	0.155
r_metal_ion_refined	0.124
r_symmetry_nbd_refined	0.111
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1340
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing