2J83 | pdb_00002j83

Ulilysin metalloprotease in complex with batimastat.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CKI	PDB ENTRY 2CKI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5		VAPOUR-DIFFUSION CRYSTALLISATION METHOD FROM SITTING DROPS CONSISTING OF 1 MICROLITER OF PROULILYSIN (5 MG/ML IN 30MM TRIS-HCL PH 7.5, 2MM DITHIOTHREITOL, 100MM NACL), 1 MICROLITER OF RESERVOIR SOLUTION (18% PEG 8000, 0.1M 2-MORPHOLINOETHANESULFONIC ACID, PH6.5, 0.2M CACL2) AND, OPTIONALLY, 0.2 MICROLITER OF 0.1M SPERMIDINE OR 30% 2, 4-METHYLPENTANEDIOL AS ADDITIVES.

Crystal Properties
Matthews coefficient	Solvent content
2.6	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.85	α = 90
b = 60.73	β = 90
c = 168.94	γ = 90

Symmetry
Space Group	C 2 2 21

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 CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	45.6	97	0.04	24.2	3.8		154616			16

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	2.11	90.3		0.07	13.9	3.8

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 2CKI	2	50	39606	520	96.4	0.161	0.161	0.17	0.211	0.21	RANDOM	17

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]
-1.25			3.05		-1.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.003
r_dihedral_angle_4_deg	14.841
r_dihedral_angle_3_deg	12.978
r_dihedral_angle_1_deg	5.969
r_scangle_it	1.927
r_scbond_it	1.204
r_angle_refined_deg	1.181
r_mcangle_it	0.68
r_mcbond_it	0.384
r_nbtor_refined	0.301
r_nbd_refined	0.183
r_symmetry_hbond_refined	0.172
r_symmetry_vdw_refined	0.147
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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	4038
Nucleic Acid Atoms
Solvent Atoms	463
Heterogen Atoms	95

Software

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