1RMZ | pdb_00001rmz

Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor NNGH at 1.3 A resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OS9	pdb entry 1OS9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	Tris, PEG6000, NNGH, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.194	α = 90
b = 62.564	β = 90
c = 37.262	γ = 90

Symmetry
Space Group	P 21 21 2

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	MARRESEARCH	double-crystal monochromator Si(111) and Si(220)	2003-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.20000	ELETTRA	5.2R

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	1.34	46.407	98.4	0.057	0.057	7.2	6.2	36295	36295			16.389

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)
	1.34	1.41	92.6		0.308	0.308	2.3	4.8	4889

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 1OS9	1.34	20	33678	33678	2578	100	0.18111	0.18111	0.17857	0.19	0.2149	0.22	RANDOM	18.214

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]
-1.38			-0.72		2.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.416
r_sphericity_free	3.899
r_scangle_it	3.53
r_sphericity_bonded	3.012
r_scbond_it	2.461
r_mcangle_it	2.067
r_angle_refined_deg	1.668
r_mcbond_it	1.373
r_rigid_bond_restr	1.352
r_angle_other_deg	1.006
r_symmetry_vdw_other	0.284
r_nbd_other	0.246
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.217
r_chiral_restr	0.197
r_xyhbond_nbd_refined	0.181
r_metal_ion_refined	0.107
r_nbtor_other	0.087
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.009
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1246
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing