6NMP | pdb_00006nmp

SFX structure of oxidized cytochrome c oxidase 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	2DYR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.8	277	36 hour crystallization in a cold room with stirring

Crystal Properties
Matthews coefficient	Solvent content
4.36	71.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.7	α = 90
b = 189.8	β = 90
c = 211.3	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	293	PIXEL	CS-PAD XPP		2016-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.306	SLAC LCLS	MFX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	40 (fs)	120		9.5 (KeV)

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1	GCVN	undefined (µl/min)	undefined (µm)

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	2.9	15	99.64	0.928	2.8	204		150666

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	2.9	2.972			0.149	0.43

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	2DYR	2.9	15	149982	7805	99.19	0.19428	0.1917	0.2014	0.24357	0.2467	RANDOM	63.835

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]
-2.46			0.72		1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.813
r_dihedral_angle_3_deg	17.699
r_dihedral_angle_4_deg	17.396
r_long_range_B_refined	10.217
r_long_range_B_other	10.212
r_dihedral_angle_1_deg	6.544
r_scangle_other	6.537
r_mcangle_it	5.887
r_mcangle_other	5.887
r_scbond_it	3.933
r_scbond_other	3.933
r_mcbond_it	3.568
r_mcbond_other	3.568
r_angle_refined_deg	1.666
r_angle_other_deg	1.115
r_chiral_restr	0.104
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.004
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	28506
Nucleic Acid Atoms
Solvent Atoms	476
Heterogen Atoms	2228

Software

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