8A9D | pdb_00008a9d

Multicrystal room temperature structure of Lysozyme collected using a double multilayer monochromator.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2LYZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
2	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
3	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
4	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
5	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
6	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
7	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
8	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
9	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
10	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
11	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
12	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
13	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
14	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
15	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
16	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
17	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
18	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
19	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
20	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.
21	LIPIDIC CUBIC PHASE	4.5	293	1M NaCl, 0.1 Na Acetate pH 4.5, 30% (v/v) PEG 400.

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.485	α = 90
b = 78.485	β = 90
c = 38.139	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	293	PIXEL	DECTRIS EIGER2 X 4M		2022-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE VMXi	0.7749	Diamond	VMXi

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.1	78.49	100	0.524	0.543	0.137	1	6.2	15.2		7390			29.63

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	2.1	2.14	100		3.26	3.369	0.834	0.299	1.2	15.99

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2LYZ	2.1	55.5	1.34	7349	735	99.82	0.199	0.1935	0.19	0.249	0.25	31.32

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.3548
f_angle_d	0.3612
f_chiral_restr	0.0372
f_plane_restr	0.0037
f_bond_d	0.0015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	977
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2.multiplex	data reduction
xia2.multiplex	data scaling
PHASER	phasing