9GCV | pdb_00009gcv

Identification of chloride ions in lysozyme at long wavelengths

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LZ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	294	100 mM sodium acetate pH 4.6, 1 M NaCl and 25% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.031	α = 90
b = 79.031	β = 90
c = 36.897	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 12M		2024-07-31	M	SINGLE WAVELENGTH
2	1	x-ray	80	PIXEL	DECTRIS PILATUS 12M		2024-07-31	M	SINGLE WAVELENGTH
3	1	x-ray	80	PIXEL	DECTRIS PILATUS 12M		2024-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	4.1328	Diamond	I23
2	SYNCHROTRON	DIAMOND BEAMLINE I23	4.5920	Diamond	I23
3	SYNCHROTRON	DIAMOND BEAMLINE I23	5.1660	Diamond	I23

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.7	79	76.8	0.07	0.99	62	17.7		2680

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.75	60.4		0.12	0.99	18.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.703	55.884	2660	138	76.305	0.189	0.1876	0.1898	0.2171	0.2174	19.357

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]
0.067			0.067		-0.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.295
r_dihedral_angle_3_deg	12.562
r_dihedral_angle_2_deg	7.242
r_dihedral_angle_1_deg	6.479
r_lrange_it	6.291
r_scangle_it	3.865
r_scbond_it	2.345
r_mcangle_it	2.186
r_angle_refined_deg	1.76
r_mcbond_it	1.278
r_nbtor_refined	0.301
r_symmetry_nbd_refined	0.233
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.12
r_metal_ion_refined	0.104
r_symmetry_xyhbond_nbd_refined	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_ext_dist_refined_b

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing