5Y89 | pdb_00005y89

Periplasmic heme-binding protein BhuT in complex with one heme (holo-1)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.8	277	2.0M Ammonium Sulfate, 0.1M Sodium Acetate

Crystal Properties
Matthews coefficient	Solvent content
6.02	79.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 199.166	α = 90
b = 199.166	β = 90
c = 117.736	γ = 120

Symmetry
Space Group	P 61 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	100	CCD	RAYONIX MX-225	mirrors	2012-07-12	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RAYONIX MX-225		2012-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.00	SPring-8	BL26B1
2	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.7375	SPring-8	BL26B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.4	50	99.6	0.101	7.3	22.1		53708

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	99.4		0.86		21

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.4	50	50964	2706	99.5	0.2014	0.2003	0.2059	0.2201	0.2236	RANDOM	52.459

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]
-0.41	-0.2		-0.41		1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.934
r_dihedral_angle_4_deg	21.184
r_dihedral_angle_3_deg	15.098
r_dihedral_angle_1_deg	5.508
r_angle_refined_deg	1.806
r_angle_other_deg	1.597
r_chiral_restr	0.138
r_bond_refined_d	0.021
r_gen_planes_other	0.021
r_gen_planes_refined	0.017
r_bond_other_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3902
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	195

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXCD	phasing
BUCCANEER	model building
HKL-2000	data reduction