4JGU

Crystal structure of Clostridium histolyticum ColH collagenase polycystic kidney-disease-like domain 2b at 1.4 Angstrom resolution in the presence of calcium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	35% (w/v) PEG 5000, 0.2M ammonium sulfate, 0.1M MES pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.387	α = 90
b = 38.869	β = 98.43
c = 54.657	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 315r		2010-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97937	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.42	22.19	96.7	0.039	33.1	3.5	37914	36663

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.44	85.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3JQU	1.42	22.19	37175	35993	1903	96.82	0.15223	0.15012	0.19133	RANDOM	14.121

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]
			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.772
r_dihedral_angle_4_deg	24.216
r_dihedral_angle_3_deg	10.491
r_scangle_it	7.177
r_dihedral_angle_1_deg	6.448
r_scbond_it	5.405
r_mcangle_it	3.916
r_mcbond_it	2.882
r_rigid_bond_restr	2.771
r_angle_refined_deg	1.737
r_nbtor_refined	0.31
r_nbd_refined	0.213
r_chiral_restr	0.137
r_symmetry_vdw_refined	0.131
r_symmetry_hbond_refined	0.096
r_xyhbond_nbd_refined	0.083
r_metal_ion_refined	0.047
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1488
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	17

Software

Software
Software Name	Purpose
HKL-3000	data collection
MLPHARE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling