6T6C | pdb_00006t6c

Complex with chitin oligomer of C-type lysozyme from the upper gastrointestinal tract of Opisthocomus hoatzin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6T5S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	293	0.1 M Citric acid pH 3.5, 3.0 M Sodium chloride, Hampton research INDEX screen no 7.

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.051	α = 90
b = 55.008	β = 90
c = 65.829	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		2012-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.25	42.247	99.9	0.105	0.998	13.4	8		38043

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.27			0.882	0.535

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	6T5S	1.25	42.247	37953	1886	99.905	0.109	0.1078	0.11	0.1343	0.13	12.994

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]
0.21			-0.235		0.025

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.84
r_rigid_bond_restr	14.052
r_dihedral_angle_3_deg	12.246
r_dihedral_angle_4_deg	11.047
r_dihedral_angle_1_deg	6.406
r_lrange_it	4.274
r_scangle_it	3.951
r_scangle_other	3.949
r_lrange_other	3.869
r_scbond_it	3.464
r_scbond_other	3.464
r_angle_other_deg	3.282
r_angle_refined_deg	2.191
r_mcangle_other	1.744
r_mcangle_it	1.69
r_mcbond_it	1.288
r_mcbond_other	1.251
r_symmetry_xyhbond_nbd_refined	0.274
r_xyhbond_nbd_refined	0.268
r_symmetry_nbd_refined	0.263
r_nbd_refined	0.252
r_symmetry_nbd_other	0.234
r_nbtor_refined	0.179
r_nbd_other	0.178
r_chiral_restr	0.164
r_symmetry_nbtor_other	0.12
r_symmetry_xyhbond_nbd_other	0.069
r_bond_other_d	0.036
r_bond_refined_d	0.018
r_gen_planes_other	0.018
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1016
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
Coot	model building