9HL1 | pdb_00009hl1

DtpB in complex with photocaged nitric oxide, 10 ms, 10 microjoule, SFX

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	6YRJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		291	50 mM HEPES pH 7.5, 150 mM Magnesium chloride, 20% (w/v) PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.073	α = 90
b = 122.875	β = 90
c = 194.936	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	300	CCD	RAYONIX MX-300		2023-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.127	SACLA	BL2

Serial Crystallography

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

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	10 (fs)	30000		10.993 (KeV)

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	1.56	103.95	100	0.994	0.096	18.1	168.6		295889

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	1.56	1.59			0.316	1.256	0.9

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 (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	1.56	44.68	293539	2027	99.89	0.20891	0.20874	0.2195	0.23363	0.2437	RANDOM	23.355

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]
-0.29			0.14		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.268
r_dihedral_angle_2_deg	8.51
r_long_range_B_refined	7.509
r_long_range_B_other	7.468
r_dihedral_angle_1_deg	6.431
r_scangle_other	5.945
r_scbond_it	3.848
r_scbond_other	3.837
r_mcangle_it	3.545
r_mcangle_other	3.545
r_mcbond_it	2.418
r_mcbond_other	2.417
r_angle_refined_deg	1.98
r_angle_other_deg	0.703
r_chiral_restr	0.104
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.006
r_bond_other_d	0.001
r_dihedral_angle_4_deg
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	13944
Nucleic Acid Atoms
Solvent Atoms	1102
Heterogen Atoms	270

Software

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