9SMC | pdb_00009smc

Acoustofluidic Serial Crystallography - Off, no acoustic focusing

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		288	140 mg/ml lysozyme in 100 mM acetate buffer, pH 3.5. 1 ml of protein solution mixed with 3 ml crystallization buffer (1.2 M NaCl, 15% (w/V) PEG4000, 100 mM acetate buffer pH 3.5) at 288 K followed by rapid mixing and incubation at 288 K.

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.4	α = 90
b = 79.4	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	295	PIXEL	DECTRIS EIGER X 16M		2024-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	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	1.96	56.44	100	0.986	0.173	4.82	201.69		9231			23.54

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.96	1.98			0.337	1.47	0.69

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	FREE R-VALUE	1.96	56.144	9208	922	99.967	0.184	0.1786	0.1889	0.2294	0.2382	24.473

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]
0.216			0.216		-0.431

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.336
r_dihedral_angle_3_deg	12.534
r_lrange_other	8.968
r_lrange_it	8.944
r_dihedral_angle_1_deg	7.588
r_scangle_it	6.904
r_scangle_other	6.9
r_scbond_it	4.48
r_scbond_other	4.48
r_mcangle_it	2.966
r_mcangle_other	2.966
r_mcbond_it	2.116
r_mcbond_other	2.109
r_angle_refined_deg	1.243
r_angle_other_deg	0.457
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.213
r_symmetry_nbd_other	0.196
r_nbd_other	0.185
r_nbtor_refined	0.178
r_symmetry_nbd_refined	0.101
r_symmetry_xyhbond_nbd_refined	0.087
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.055
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing
PHENIX	refinement
PDB-REDO	refinement
CrystFEL	data collection