5O4C | pdb_00005o4c

From macrocrystals to microcrystals: a strategy for membrane protein serial crystallography

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	5NJ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	277	Crystals grown from one round of seeding. Macrocrystal growth: 25 ul sitting drop. 10 ul 10 mg/ml protein, 15 ul precipitate solution Precipitate solution: 3.6 M Ammonium sulphate, 20 mM sodium phosphate buffer pH 6.8. 6 % w:v heptane-1-2-3-triol. 1 ml 2 M Ammonium sulphate reservoir Growth at 277 K for 4 days. Macrocrystals crushed into seed stock Micro-crystals 17.5 ul sitting drop. 10 ul 8.5 mg/ml protein, 7.5 ul precipitate solution 1 ml 2 M Ammonium sulphate solution

Crystal Properties
Matthews coefficient	Solvent content
5.52	77.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 226.4	α = 90
b = 226.4	β = 90
c = 113.7	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	CS-PAD CXI-1		2015-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.89	SLAC LCLS	CXI

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	2.8	36.9	100	0.997	10.4	1342		69325			97.4

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	2.8	2.89	100		0.408	0.88	361

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	5NJ4	2.8	36.9	69325	3626	99.94	0.16665	0.16507	0.1723	0.19612	0.1977	RANDOM	96.859

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]
1.6			1.6		-3.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.947
r_dihedral_angle_4_deg	15.906
r_dihedral_angle_3_deg	14.97
r_long_range_B_refined	10.051
r_long_range_B_other	10.051
r_scangle_other	8.063
r_mcangle_other	7.311
r_mcangle_it	7.31
r_dihedral_angle_1_deg	6.101
r_scbond_it	5.488
r_scbond_other	5.488
r_mcbond_it	5.24
r_mcbond_other	5.237
r_angle_refined_deg	2.052
r_angle_other_deg	0.987
r_chiral_restr	0.077
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9347
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	836

Software

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