9HS8 | pdb_00009hs8

Cytochrome c prime beta from Methylococcus capsulatus (Bath) in complex with nitric oxide from proli NONOate

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	6HIH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		291	Final concentrations: 20 mg/mL protein, 50 mM HEPES pH 7.5, 34 % (v/v) polyethylene glycol 550, 500 mM MES pH 6.5, 5 mM ZnSO4.

Crystal Properties
Matthews coefficient	Solvent content
2.97	63.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.441	α = 90
b = 107.441	β = 90
c = 107.441	γ = 90

Symmetry
Space Group	P 21 3

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 PILATUS3 6M		2019-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.969	Diamond	I24

Serial Crystallography

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

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1	Oxford silicon chip			Geobrick and Smaract

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	undefined (fs)			undefined (KeV)

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

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	1.85	76.09	100	0.998	0.068	11	175.4		35508

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	1.85	1.88	100		0.534	0.936	0.9	137.3

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	1.85	76.088	35507	1729	100	0.156	0.1551	0.1551	0.1795	0.1796	34.669

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
r_dihedral_angle_6_deg	15.336
r_dihedral_angle_3_deg	13.068
r_lrange_it	9.82
r_scangle_it	8.392
r_dihedral_angle_1_deg	7.056
r_dihedral_angle_2_deg	6.589
r_scbond_it	5.663
r_mcangle_it	5.039
r_mcbond_it	3.682
r_angle_refined_deg	2.553
r_nbtor_refined	0.316
r_metal_ion_refined	0.245
r_symmetry_nbd_refined	0.212
r_nbd_refined	0.208
r_chiral_restr	0.147
r_xyhbond_nbd_refined	0.139
r_symmetry_xyhbond_nbd_refined	0.113
r_bond_refined_d	0.013
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2139
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	104

Software

Software
Software Name	Purpose
DIALS	data reduction
xia2	data reduction
MOLREP	phasing
Coot	model building
REFMAC	refinement
xia2	data scaling