8FXD | pdb_00008fxd

Rubrerythrin from B. pseudomallei: manganese-bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	0.138 M Li2SO4, 0.92 M BTP, pH 8, 22.08% PEG 3350, 0.8 mM MnCl2

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 201.874	α = 90
b = 201.874	β = 90
c = 69.025	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2022-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.97934	NSLS-II	17-ID-2

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	1.58	29.14	93.7	0.092	0.115	0.069	0.998	9.5	5.2		108953

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	1.58	1.692	59.3		0.833	1.161	0.807	0.457		3.1

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	1.58	29.14	108953	5467	93.7	0.149	0.1477	0.16	0.1755	0.19	19.178

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]
0.003	0.001		0.003		-0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.938
r_dihedral_angle_3_deg	14.738
r_lrange_it	6.82
r_dihedral_angle_2_deg	6.713
r_lrange_other	6.578
r_scangle_it	5.823
r_scangle_other	5.822
r_dihedral_angle_1_deg	4.57
r_scbond_it	3.629
r_scbond_other	3.628
r_mcangle_other	2.536
r_mcangle_it	2.533
r_mcbond_it	1.824
r_mcbond_other	1.82
r_angle_refined_deg	1.529
r_angle_other_deg	0.548
r_symmetry_nbd_refined	0.38
r_nbd_other	0.343
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.188
r_symmetry_nbd_other	0.174
r_symmetry_xyhbond_nbd_refined	0.123
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6443
Nucleic Acid Atoms
Solvent Atoms	874
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing