4GUY | pdb_00004guy

Human MMP12 catalytic domain in complex withN-Hydroxy-2-(2-(4-methoxyphenyl)ethylsulfonamido)acetamide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y93	PDB ENTRY 1Y93

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	0.1M TRIS-HCL, 30% PEG 6000, 1M LICL, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.989	α = 90
b = 61.107	β = 114.5
c = 54.213	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	OXFORD ONYX CCD	GRAPHITE	2006-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION ENHANCE ULTRA	1.5406

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	30.56	98.2	0.146	0.146	5	4.9	10122	10122			11.53

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	2.1	87.9		0.383	0.383	2.3	1.9

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1Y93	2	30.56	9209	9209	913	98.16	0.23324	0.23324	0.2271	0.2268	0.29268	0.2909	RANDOM	13.6

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]
-0.23		-0.77	-0.42		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.296
r_dihedral_angle_4_deg	16.86
r_dihedral_angle_3_deg	15.034
r_dihedral_angle_1_deg	7.094
r_scangle_it	3.976
r_scbond_it	3
r_mcangle_it	2.045
r_angle_refined_deg	1.696
r_mcbond_it	1.358
r_nbtor_refined	0.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.296
r_dihedral_angle_4_deg	16.86
r_dihedral_angle_3_deg	15.034
r_dihedral_angle_1_deg	7.094
r_scangle_it	3.976
r_scbond_it	3
r_mcangle_it	2.045
r_angle_refined_deg	1.696
r_mcbond_it	1.358
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.262
r_nbd_refined	0.243
r_xyhbond_nbd_refined	0.226
r_symmetry_hbond_refined	0.186
r_metal_ion_refined	0.165
r_chiral_restr	0.109
r_bond_refined_d	0.014
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1238
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	24

Software

Software
Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.