9HQT | pdb_00009hqt

SFX structure of cytochrome c prime beta from Methylococcus capsulatus (Bath)

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 = 107.1	α = 90
b = 107.1	β = 90
c = 107.1	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	300	CCD	MPCCD		2019-06-26	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

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

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	10 (fs)	30	2.56	11 (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	1.8	33.89	100	0.938	0.204	4	233.7		38160

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	1.9	1.93	100		0.639	0.492	2.1	159.9

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	1.8	33.89	38147	1886	99.945	0.191	0.19	0.19	0.219	0.2191	29.718

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	16.031
r_dihedral_angle_3_deg	12.124
r_lrange_it	7.434
r_lrange_other	7.401
r_dihedral_angle_1_deg	6.846
r_dihedral_angle_2_deg	6.572
r_scangle_it	4.825
r_scangle_other	4.823
r_scbond_other	3.124
r_scbond_it	3.123
r_angle_refined_deg	2.317
r_mcangle_other	2.309
r_mcangle_it	2.307
r_mcbond_it	1.611
r_mcbond_other	1.611
r_angle_other_deg	0.628
r_nbd_refined	0.204
r_symmetry_nbd_other	0.201
r_nbd_other	0.195
r_nbtor_refined	0.182
r_symmetry_nbd_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.124
r_xyhbond_nbd_refined	0.121
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.087
r_bond_refined_d	0.017
r_gen_planes_other	0.014
r_gen_planes_refined	0.013
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2126
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	105

Software

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