8FVV | pdb_00008fvv

Rubrerythrin from B. pseudomallei: iron-bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other	8FUH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.75	273	0.15 M lithium sulfate 30% PEG 3350 0.1 M BTP pH 6.75 1 mM iron chloride

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 202.17	α = 90
b = 202.17	β = 90
c = 69.825	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		2022-10-28	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	1.93	29.9	92.4	0.23	0.241	0.073	0.995	8.9	10.8		61079		2	13.99

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	2.07	61.4		1.898	0.607	0.597	1.5	10.7

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.93	29.9	61079	2998	92.4	0.163	0.161	0.17	0.209	0.21	RANDOM	24.663

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]
-0.013	-0.006		-0.013		0.042

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.485
r_dihedral_angle_3_deg	15.019
r_lrange_it	6.688
r_lrange_other	6.441
r_dihedral_angle_2_deg	6.339
r_dihedral_angle_1_deg	5.002
r_scangle_it	4.912
r_scangle_other	4.912
r_mcangle_other	3.147
r_mcangle_it	3.146
r_scbond_it	3.08
r_scbond_other	3.08
r_mcbond_it	2.066
r_mcbond_other	2.066
r_angle_refined_deg	1.38
r_angle_other_deg	0.479
r_nbd_refined	0.23
r_nbd_other	0.21
r_symmetry_nbd_refined	0.208
r_xyhbond_nbd_refined	0.206
r_nbtor_refined	0.188
r_symmetry_nbd_other	0.179
r_symmetry_xyhbond_nbd_refined	0.143
r_metal_ion_refined	0.1
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6464
Nucleic Acid Atoms
Solvent Atoms	800
Heterogen Atoms	12

Software

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