1RM8 | pdb_00001rm8

Crystal structure of the catalytic domain of MMP-16/MT3-MMP: Characterization of MT-MMP specific features

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BQQ	Pdb code 1bqq

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Tris-HCl, Sodium/potassium tartrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.21	α = 90
b = 51.21	β = 90
c = 149.368	γ = 90

Symmetry
Space Group	P 43 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	MARRESEARCH	mirrors	1999-04-07	M	SINGLE WAVELENGTH
2	1	100	CCD	MARRESEARCH		1999-09-18

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	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 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	1.8	16.6	96.7	0.083	5.5			18455		2.2	23.51

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	1.8	1.9	91.1		0.327	0.327	2.2		1090

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	Pdb code 1bqq	1.8	16.6	1	18455	900	96.7	0.20907	0.20907	0.20768	0.23644	Random	23.509

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]
0.07			0.07		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.712
r_bond_refined_d	0.017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1338
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	36

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.