4JRW

Crystal structure of Clostridium histolyticum colg collagenase PKD domain 2 at 1.6 Angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C4X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	277	MPD, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.95	α = 90
b = 48.992	β = 90
c = 70.858	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	CCD	RIGAKU SATURN 92		2008-04-05	M	SINGLE WAVELENGTH
2	1	x-ray	93	CCD	ADSC QUANTUM 315		2008-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5478
2	SYNCHROTRON	APS BEAMLINE 19-BM	0.919457	APS	19-BM

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
1,2	1.6	37.9	99.9	0.061	30.9	4.1	39924	39884

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.58	1.69	99.8

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	2C4X	1.6	37.9	20556	20159	1092	99.9	0.1782	0.17649	0.20951	RANDOM	20.237

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]
0.49			-0.29		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.237
r_dihedral_angle_4_deg	21.012
r_dihedral_angle_3_deg	15.157
r_scangle_it	6.166
r_dihedral_angle_1_deg	5.557
r_scbond_it	3.795
r_mcangle_it	2.492
r_angle_refined_deg	2.042
r_mcbond_it	1.479
r_chiral_restr	0.166
r_bond_refined_d	0.024
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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	1290
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	1

Software

Software
Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
CCP4	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CCP4	phasing