4U6T | pdb_00004u6t

Crystal structure of the Clostridium histolyticum colH collagenase polycystic kidney disease-like domain 2a at 1.76 Angstrom resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	290	3 M ammonium sulfate, 0.1 M MES pH 4.5, 15% (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.33	α = 90
b = 88.33	β = 90
c = 123.56	γ = 120

Symmetry
Space Group	P 61

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	1.76	65.04	99.5	0.068	11.5	4.7		53717

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	1.76	1.82	95.7		0.374	2.3	2.12	5129

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	1.76	65.04	53663	2731	99.36	0.2099	0.2067	0.21	0.2715	0.25	RANDOM	31.334

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]
0.52	0.26		0.52		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.277
r_scangle_it	14.353
r_dihedral_angle_3_deg	13.482
r_scbond_it	12.909
r_dihedral_angle_1_deg	7.304
r_mcangle_it	5.822
r_mcbond_it	4.018
r_angle_refined_deg	1.229
r_chiral_restr	0.119
r_bond_refined_d	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.277
r_scangle_it	14.353
r_dihedral_angle_3_deg	13.482
r_scbond_it	12.909
r_dihedral_angle_1_deg	7.304
r_mcangle_it	5.822
r_mcbond_it	4.018
r_angle_refined_deg	1.229
r_chiral_restr	0.119
r_bond_refined_d	0.011
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2684
Nucleic Acid Atoms
Solvent Atoms	1106
Heterogen Atoms	110

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.