2OXW | pdb_00002oxw

Human MMP-12 complexed with the peptide IAG

X-RAY DIFFRACTION

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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	0.1 M Tris-HCl, 30% PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.888	α = 90
b = 60.358	β = 115.73
c = 54.521	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 315	Double crystal, Si(111) or Si(311)	2006-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.15	49.08	94.6	0.059	0.059	4.2	6.8	50850	50850			11.08

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)
	1.15	1.21	91.1		0.156	0.156	4.1	6.8	7153

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	1.15	36.96	46196	46196	4653	100	0.19942	0.19942	0.19713	0.2	0.2225	0.23	RANDOM	14.16

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]
-0.07		-0.08	0.11		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.255
r_dihedral_angle_4_deg	10.841
r_dihedral_angle_3_deg	10.507
r_dihedral_angle_1_deg	5.769
r_sphericity_free	3.282
r_scangle_it	2.304
r_sphericity_bonded	2.019
r_rigid_bond_restr	1.756
r_scbond_it	1.655
r_mcangle_it	1.315
r_angle_refined_deg	1.093
r_angle_other_deg	0.978
r_mcbond_it	0.897
r_mcbond_other	0.357
r_nbd_refined	0.223
r_symmetry_vdw_other	0.2
r_symmetry_vdw_refined	0.195
r_nbd_other	0.186
r_nbtor_refined	0.185
r_symmetry_hbond_refined	0.158
r_xyhbond_nbd_refined	0.097
r_nbtor_other	0.084
r_metal_ion_refined	0.084
r_chiral_restr	0.067
r_bond_other_d	0.009
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1255
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	5

Software

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