6KXM | pdb_00006kxm

Crystal structure of D157N mutant of Chitiniphilus shinanonensis chitinase ChiL (CsChiL) complexed with N,N'-diacetylchitobiose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6KST

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293.15	0.1 M Bis-Tris, 0.2 M NaCl, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.266	α = 90
b = 81.351	β = 90
c = 131.113	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	97	CCD	ADSC QUANTUM 270	Focusing mirror	2015-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.000	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.95	50	97.8	0.102	0.112	0.046	8.8	5.7		54922

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.02	99		0.682	0.752	0.312	0.93	2.92	5.7

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	6KST	1.95	34.59	50006	2734	96.29	0.251	0.2485	0.25	0.298	0.3	RANDOM	31.626

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]
-2.18			5.16		-2.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.774
r_dihedral_angle_3_deg	14.994
r_dihedral_angle_4_deg	13.694
r_dihedral_angle_1_deg	7.611
r_angle_refined_deg	1.494
r_angle_other_deg	1.278
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.774
r_dihedral_angle_3_deg	14.994
r_dihedral_angle_4_deg	13.694
r_dihedral_angle_1_deg	7.611
r_angle_refined_deg	1.494
r_angle_other_deg	1.278
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5796
Nucleic Acid Atoms
Solvent Atoms	372
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.