1Y93 | pdb_00001y93

Crystal structure of the catalytic domain of human MMP12 complexed with acetohydroxamic acid at atomic resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	Tris, PEG 6000, ACETOHYDROXAMIC ACID, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.913	α = 90
b = 59.552	β = 115.14
c = 53.497	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	MARRESEARCH	double-crystal, Si(111) and Si(220)	2004-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	0.99993	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	1.02	48.4	97.6	0.057	0.057	5.5	3.7	70833	70833			6.63

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	1.02	1.08	84.9		0.251	0.251	2.7	3.1	8671

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 1RMZ	1.03	13.99	65283	65283	5517	100	0.1566	0.1566	0.15563	0.16	0.16787	0.17	RANDOM	8.688

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]
0.04		-0.12	0.09		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.082
r_dihedral_angle_4_deg	14.416
r_dihedral_angle_3_deg	11.832
r_dihedral_angle_1_deg	6.382
r_sphericity_free	3.907
r_scangle_it	3.254
r_sphericity_bonded	2.65
r_scbond_it	2.21
r_mcangle_it	1.635
r_angle_refined_deg	1.379
r_mcbond_it	1.125
r_rigid_bond_restr	1.104
r_angle_other_deg	0.721
r_mcbond_other	0.523
r_nbd_refined	0.216
r_nbtor_refined	0.2
r_symmetry_vdw_other	0.199
r_nbd_other	0.185
r_symmetry_vdw_refined	0.183
r_symmetry_hbond_refined	0.146
r_xyhbond_nbd_refined	0.129
r_metal_ion_refined	0.11
r_nbtor_other	0.09
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1238
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	10

Software

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