Experiment: 4FVL

Human collagenase 3 (MMP-13) full form with peptides from pro-domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FU4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SLOW COOLING	7.5	277	propeptide impurity induces crystallization on cold storage cryoprotectant: 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10K, 10% PCTP 80/20, 0.2 M NaCl, pH 7.5, SLOW COOLING, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.78	α = 90
b = 157.27	β = 90
c = 105.55	γ = 90

Symmetry
Space Group	C 2 2 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	mirrors	2010-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.980110	SOLEIL	PROXIMA 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	2.44	50	95.7	0.165	0.15	11.15	5.82	39481	37803		-3	43.396

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	2.44	2.58	96.6		1.025	0.92	2.71	5.69	6101

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	4FU4	2.436	49.114	-3	2	39472	37795	1890	95.75	0.1685	0.1656	0.1675	0.223	0.2235	RANDOM	33.07

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.547
f_angle_d	1.196
f_chiral_restr	0.083
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6300
Nucleic Acid Atoms
Solvent Atoms	234
Heterogen Atoms	280

Software

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