9HYZ | pdb_00009hyz

McCP in complex with photocaged nitric oxide, dark control, SSX

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
2.95	63.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.314	α = 90
b = 107.314	β = 90
c = 107.314	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 EIGER2 X CdTe 9M		2023-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.620	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	2.2	75.998	100	0.974	0.184	9	40		21205

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	2.2	2.24			0.373	0.753	1.9

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	2.2	75.998	21194	1071	100	0.194	0.1922	0.1922	0.2307	0.231	41.162

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_3_deg	13.912
r_dihedral_angle_6_deg	12.585
r_lrange_it	8.228
r_dihedral_angle_1_deg	7.054
r_scangle_it	6.555
r_dihedral_angle_2_deg	5.698
r_scbond_it	4.121
r_mcangle_it	3.838
r_mcbond_it	2.49
r_angle_refined_deg	2.112
r_symmetry_nbd_refined	0.373
r_nbtor_refined	0.309
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.112
r_symmetry_xyhbond_nbd_refined	0.096
r_gen_planes_refined	0.009
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2146
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	94

Software

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