7S4W | pdb_00007s4w

Serial Macromolecular Crystallography at ALBA Synchrotron Light Source - Lysozyme

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		298	0.1 M sodium acetate pH 3.0, 18 % (w/v) sodium chloride, 6% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79	α = 90
b = 79	β = 90
c = 38.2	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	298	PIXEL	DECTRIS PILATUS 6M		2018-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97918	ALBA	XALOC

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	LCP Injection	injection

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1		undefined (µl/min)	undefined (µm)

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	2.1	38.2	100	0.996	9.8	679		7498			37.4

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	2.1	2.17			0.207	0.5	161

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1VDS	2.1	35.35	6723	741	99.97	0.18359	0.17847	0.19	0.23225	0.21	RANDOM	47.711

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]
-0.64			-0.64		1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.69
r_dihedral_angle_4_deg	18.747
r_dihedral_angle_3_deg	15.004
r_long_range_B_refined	6.713
r_long_range_B_other	6.711
r_dihedral_angle_1_deg	6.542
r_scangle_other	5.398
r_scbond_it	3.563
r_scbond_other	3.56
r_mcangle_other	3.261
r_mcangle_it	3.26
r_mcbond_it	2.482
r_mcbond_other	2.478
r_angle_refined_deg	1.389
r_angle_other_deg	1.142
r_chiral_restr	0.081
r_bond_refined_d	0.009
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	17
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
Aimless	data scaling
MOLREP	phasing