9V3J | pdb_00009v3j

Time-Resolved mixing crystallography structure of 3-5 micrometers Lysozyme microcrystals with 226 mM N-Acetyl-D-glucosamine at 9.7 seconds delay

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	3	290	8% PEG 6000, 4.8 M NaCl, and 0.1M sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.45	α = 90
b = 79.45	β = 90
c = 38.15	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	CCD	MPCCD		2023-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.24	SACLA	BL2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.68	39.68	100	0.969	7.31	187.4		14488

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.68	1.7			0.7053

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.68	35.53	1.37	14444	721	99.97	0.1905	0.1887	0.1889	0.2231	0.2243

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	9.74
f_angle_d	1.407
f_chiral_restr	0.089
f_bond_d	0.013
f_plane_restr	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	998
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	18

Software

Software
Software Name	Purpose
PHENIX	refinement
CrystFEL	data scaling
CrystFEL	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction