8BRL

Room temperature crystal structure of cytochrome c' from Hydrogenophilus thermoluteolus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	30% PEG 8000, 0.2 M lithium sulfate, 0.1 M sodium acetate pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.9	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.536	α = 90
b = 83.536	β = 90
c = 88.566	γ = 120

Symmetry
Space Group	P 62 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 EIGER2 X 4M		2022-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE VMXi	0.7749	Diamond	VMXi

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.88	56.09	100	0.459	0.469	0.093	0.995	7.9	22.3		15440

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.91	100		5.496	5.683	1.401	0.258	0.6	15.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5B3I	1.88	56.09	14620	777	99.9	0.17918	0.17791	0.20314	RANDOM	31.553

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]
0.04	0.02		0.04		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.968
r_dihedral_angle_4_deg	21.823
r_dihedral_angle_3_deg	17.295
r_long_range_B_refined	9.379
r_long_range_B_other	9.35
r_scangle_other	7.873
r_dihedral_angle_1_deg	5.893
r_scbond_it	5.247
r_scbond_other	5.095
r_mcangle_it	4.162
r_mcangle_other	4.159
r_mcbond_it	2.763
r_mcbond_other	2.762
r_angle_refined_deg	2.32
r_angle_other_deg	1.481
r_chiral_restr	0.158
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
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	1029
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2.multiplex	data scaling
PHASER	phasing