3GXK | pdb_00003gxk

The crystal structure of g-type lysozyme from Atlantic cod (Gadus morhua L.) in complex with NAG oligomers sheds new light on substrate binding and the catalytic mechanism. Native structure to 1.9

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	154L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	48-53% ammonium sulphate, 5mM CoCl2, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.12	α = 90
b = 75.39	β = 92.92
c = 78.37	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	100	CCD	MARMOSAIC 225 mm CCD		2007-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	48.02	99.5	0.06	0.06	9.4	4.5	50454	50202		2	18.99

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	2	96.9		0.221	0.221	3.3	4.3	7068

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	154L	1.9	48.02	47647	2548	99.53	0.19412	0.19108	0.19	0.25136	0.25	RANDOM	18.764

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]
0.53		-1.58	-0.79		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.841
r_dihedral_angle_4_deg	20.667
r_dihedral_angle_3_deg	16.314
r_dihedral_angle_1_deg	6.108
r_scangle_it	3.895
r_scbond_it	2.658
r_mcangle_it	1.646
r_angle_refined_deg	1.563
r_mcbond_it	1.083
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.841
r_dihedral_angle_4_deg	20.667
r_dihedral_angle_3_deg	16.314
r_dihedral_angle_1_deg	6.108
r_scangle_it	3.895
r_scbond_it	2.658
r_mcangle_it	1.646
r_angle_refined_deg	1.563
r_mcbond_it	1.083
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.219
r_nbd_refined	0.214
r_symmetry_hbond_refined	0.187
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.118
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5731
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	2

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	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.