9GK1 | pdb_00009gk1

SSX structure of human cytochrome P450 3A4 at room temperature

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	4TQN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	293.15	Final droplet contained 6%v/v PEG3350, 50 mM sodium malonate, 15 mg/mL CYP3A4, 25 mM KPi pH 7.3, 100 mM KCl, 1 mM DTT, 0.5 mM EDTA, 10%v/v glycerol, 1%v/v DMSO and 100 uM beta-napthoflavone. The droplet was equillibrated against a reservoir of 100 mM sodium malonate and 12%v/v PEG3350. The crystalisation droplet swelled due to high glycerol concentration.

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.95	α = 90
b = 103.74	β = 90
c = 128.64	γ = 90

Symmetry
Space Group	I 2 2 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	DECTRIS EIGER X 16M	BioMAX components: undulator, two front-end beam position monitors, front-end fluorescent screen, optics hutch fixed mask, double-crystal monochromator, fluorescent screen, NanoBPM, slits, vertical focusing mirror, horizontal focusing mirror, NanoBPM, beam conditioning unit (BCU), sample and detector. The BCU chamber includes slits, diagnostics, two diamond beam position monitors, attenuators, shutter, slits and diagnostics.	2022-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.976	MAX IV	BioMAX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	Serial X SPINE-mounted Kapton membrane sandwich on a plastic frame	fixed target

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1	8 x 1 uL crystal slurry on kapton films	Serial X SPINE-mounted Kapton membrane sandwich on a plastic frame	SPINE-compatible	Arinax Microdiffractomer MD3-down	Arinax Microdiffractomer MD3-down mini-kappagoniometer head

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	52670		52670

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	2.95	80.75	100	0.9953922	0.0543	14.758752	416.91		11603			121.39

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	2.95	3	100		0.5453646	0.7304	1	282.9

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	2.95	80.75	11009	589	99.94	0.24643	0.24369	0.2494	0.29508	0.301	RANDOM	143.605

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]
-1.74			0.1		1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.474
r_dihedral_angle_3_deg	19.105
r_dihedral_angle_4_deg	13.977
r_dihedral_angle_1_deg	4.682
r_angle_refined_deg	1.208
r_mcangle_it	1.069
r_mcangle_other	1.069
r_angle_other_deg	0.975
r_scangle_other	0.939
r_mcbond_it	0.573
r_mcbond_other	0.573
r_scbond_it	0.319
r_scbond_other	0.319
r_chiral_restr	0.035
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.002
r_bond_other_d	0.001
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	3738
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data scaling
CrystFEL	data reduction
PHASER	phasing
Coot	model building