Experiment: 2PJT

Crystal structure of the catalytic domain of MMP-13 complexed with WAY-344

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	300	20% PEG 3350, 0.2M MgCl2, 0.1M Hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.352	α = 90
b = 35.789	β = 108.94
c = 139.405	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	ADSC QUANTUM 4	Crystal Logic diffractometer consisting of a mini-kappa goniometer		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.00000	NSLS	X26C

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	2.7	50	88.9	0.1	0.1	11.4	3.42	15836	15836			-0.5

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)
	2.7	2.8	54.2		0.402	0.402	1.88	2	1746

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1ZTQ	2.8	19.95	15836	14875	759	92.5	0.221	0.212	0.212	0.27	RANDOM	41.9

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]
11.44		23.04	-14.51		3.07

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	28.7
c_scangle_it	2.06
c_improper_angle_d	1.68
c_mcangle_it	1.55
c_angle_deg	1.4
c_scbond_it	1.31
c_mcbond_it	0.96
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5154
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	146

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
HKL-2000	data scaling
AMoRE	phasing