4U7K | pdb_00004u7k

Crystal structure of the Clostridium histolyticum colH collagenase polycystic kidney disease-like domain 2a in the presence of calcium at 1.9 Angstrom resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	290	0.2 M magnesium chloride, 0.1 M Tris-HCl pH 8.5, and 30% (w/v) PEG 4000. Crystals soaked in 0.2 M magnesium chloride, 0.05 M calcium chloride, 0.1 M Tris-HCl pH 8.5, and 15% (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.32	α = 90
b = 87.61	β = 116.04
c = 104.35	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	113	CCD	RIGAKU SATURN 92	CCD	2013-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54180

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	1.91	22.11	96.4	0.046	13.8	3.63		61851

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	1.91	1.98	93.8		0.31	3	3.11	6009

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.91	93.76	61839	3119	96.28	0.1651	0.1629	0.17	0.2073	0.22	RANDOM	33.81

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]
-0.4		-0.48	0.63		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.842
r_dihedral_angle_3_deg	14.118
r_scangle_it	11.227
r_dihedral_angle_1_deg	7.059
r_scbond_it	6.771
r_mcangle_it	3.93
r_mcbond_it	2.656
r_angle_refined_deg	1.062
r_chiral_restr	0.1
r_gen_planes_refined	0.019

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.842
r_dihedral_angle_3_deg	14.118
r_scangle_it	11.227
r_dihedral_angle_1_deg	7.059
r_scbond_it	6.771
r_mcangle_it	3.93
r_mcbond_it	2.656
r_angle_refined_deg	1.062
r_chiral_restr	0.1
r_gen_planes_refined	0.019
r_bond_refined_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5368
Nucleic Acid Atoms
Solvent Atoms	967
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
PDB_EXTRACT	data extraction
d*TREK	data scaling

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.