6T5S | pdb_00006t5s

Apo form 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	1GFT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	150 nl of protein was mixed with 150 nl of mother liquor solution. Crystals grew in 0.1 M MIB system (malonic acid, imidazole, boric acid) pH 4.0 and 25% Peg 3350

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.973	α = 90
b = 54.895	β = 90
c = 65.319	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		2009-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

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	1.5	42.06	99.8	0.074	0.998	12.3	5		21950

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	1.5	1.53			0.535	0.646	1.9

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	MOLECULAR REPLACEMENT	FREE R-VALUE	1gft	1.5	42.06	21899	1108	99.727	0.118	0.1156	0.12	0.1657	0.17	15.187

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]
-0.046			-0.08		0.126

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.751
r_rigid_bond_restr	12.56
r_dihedral_angle_3_deg	11.733
r_dihedral_angle_4_deg	8.24
r_dihedral_angle_1_deg	6.717
r_lrange_it	4.591
r_lrange_other	4.589
r_scangle_it	3.178
r_scangle_other	3.176
r_scbond_it	2.7
r_scbond_other	2.697
r_angle_other_deg	2.429
r_mcangle_other	2.225
r_mcangle_it	2.203
r_mcbond_it	1.802
r_mcbond_other	1.772
r_angle_refined_deg	1.744
r_symmetry_xyhbond_nbd_refined	0.277
r_symmetry_nbd_refined	0.266
r_nbd_refined	0.239
r_symmetry_nbd_other	0.223
r_xyhbond_nbd_refined	0.211
r_nbd_other	0.185
r_nbtor_refined	0.18
r_chiral_restr	0.113
r_symmetry_nbtor_other	0.076
r_bond_other_d	0.037
r_bond_refined_d	0.015
r_gen_planes_other	0.013
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1000
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing