2XS3 | pdb_00002xs3

Structure of karilysin catalytic MMP domain

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	CRYSTALLIZATION ASSAYS WERE PERFORMED BY THE SITTING-DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTIONS WERE PREPARED BY A TECAN ROBOT AND CRYSTALLIZATION DROPS WERE DISPENSED ON 96X2-WELL MRC PLATES (INNOVADYNE) BY A CARTESIAN (GENOMIC SOLUTIONS) NANODROP ROBOT AT THE HIGH-THROUGHPUT CRYSTALLOGRAPHY PLATFORM AT BARCELONA SCIENCE PARK. CRYSTALS SUITABLE FOR STRUCTURE ANALYSIS WERE OBTAINED FOR UNBOUND KLY18 IN A BRUKER STEADY-TEMPERATURE CRYSTAL FARM AT 20C FROM DROPS CONTAINING 100NL OF PROTEIN SOLUTION (AT 9MG ML-1 IN 5MM TRIS-HCL, PH8.0, 0.02% SODIUM AZIDE) AND 100NL OF 45% 2-METHYL-2,4-PENTANEDIOL, 0.2M AMMONIUM ACETATE, 0.1M TRIS-HCL, PH8.5 AS RESERVOIR SOLUTION.

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.37	α = 90
b = 53.11	β = 134.55
c = 86.3	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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.4	45.3	99.3	0.09	14.8	4.1		15411			38.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53	95.9		0.51	2.5	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	PDB ENTRY 1MNC	2.4	50	14703	708	99.28	0.19197	0.18877	0.2	0.25872	0.26	RANDOM	33.731

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]
3.2		2.49	-1.7		1.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.332
r_dihedral_angle_3_deg	17.064
r_dihedral_angle_4_deg	15.179
r_dihedral_angle_1_deg	6.729
r_scangle_it	2.264
r_scbond_it	1.46
r_angle_refined_deg	1.321
r_mcangle_it	1.109
r_angle_other_deg	0.886
r_mcbond_it	0.603
r_mcbond_other	0.106
r_chiral_restr	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2702
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing