3JQX | pdb_00003jqx

Crystal structure of Clostridium histolyticum colH collagenase collagen binding domain 3 at 2.2 Angstrom resolution in the presence of calcium and cadmium

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O8O	2o8o ColG-3b collagen binding domain

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	sodium acetate, CdSO4,CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.567	α = 90
b = 64.589	β = 90
c = 96.01	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	100	CCD	ADSC QUANTUM 315			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	2.2	30	98.7	0.12	9.6	13.9		18873	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.5	97.7		0.54	2.4	3.4	1431

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	2o8o ColG-3b collagen binding domain	2.2	28.68	18872	1017	98.73	0.17941	0.17571	0.18	0.2502	0.25	RANDOM	20.309

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]
0.02			-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.907
r_dihedral_angle_4_deg	23.297
r_dihedral_angle_3_deg	16.181
r_dihedral_angle_1_deg	6.994
r_scangle_it	4.903
r_scbond_it	3.338
r_mcangle_it	2.087
r_angle_refined_deg	1.889
r_mcbond_it	1.183
r_nbtor_refined	0.321

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.907
r_dihedral_angle_4_deg	23.297
r_dihedral_angle_3_deg	16.181
r_dihedral_angle_1_deg	6.994
r_scangle_it	4.903
r_scbond_it	3.338
r_mcangle_it	2.087
r_angle_refined_deg	1.889
r_mcbond_it	1.183
r_nbtor_refined	0.321
r_symmetry_hbond_refined	0.29
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.184
r_symmetry_vdw_refined	0.178
r_chiral_restr	0.129
r_metal_ion_refined	0.115
r_bond_refined_d	0.022
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2801
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	12

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.