3GH9

Crystal structure of EDTA-treated BdbD (Oxidised)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EU3	PDB ENTRY 3EU3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	25-27 % PEG2000, 100mM Ammonium Acetate, 100mM MES, pH6.5, 100uM EDTA, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.55	α = 90
b = 43.57	β = 107.38
c = 54.56	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100					M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9798	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.69	36.79	92.7	0.052	19.9	5.4	18095	18095	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.69	1.78	66.2		0.286	3.5	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3EU3	1.69	36.79	18095	17169	914	92.58	0.19784	0.19503	0.19	0.25004	0.24	RANDOM	21.136

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]
-0.25		-0.16	1.07		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.169
r_dihedral_angle_3_deg	14.292
r_dihedral_angle_4_deg	13.672
r_dihedral_angle_1_deg	4.956
r_sphericity_free	4.276
r_sphericity_bonded	3.319
r_scangle_it	3.184
r_scbond_it	2.027
r_mcangle_it	1.393
r_angle_refined_deg	1.225
r_rigid_bond_restr	1.194
r_mcbond_it	0.822
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1620
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	5

Software

Software
Software Name	Purpose
ADSC	data collection
BP3	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
BP3	phasing