5JP6 | pdb_00005jp6

Bdellovibrio bacteriovorus peptidoglycan deacetylase Bd3279

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C1G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1M Na cacodylate pH 6.5 0.2M Mg acetate 20% w/v/ PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.434	α = 90
b = 112.434	β = 90
c = 79.859	γ = 120

Symmetry
Space Group	P 61

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 PILATUS 6M		2012-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97950	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.5	97.37	99.9	25.1	14		91430

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2C1G	1.5	97.37	86803	4581	99.81	0.1458	0.1448	0.1453	0.1668	0.1669	RANDOM	29.028

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]
0.06	0.03		0.06		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	34.609
r_dihedral_angle_2_deg	34.399
r_sphericity_bonded	15.856
r_dihedral_angle_3_deg	12.687
r_dihedral_angle_4_deg	12.221
r_dihedral_angle_1_deg	5.558
r_rigid_bond_restr	4.286
r_mcangle_it	3.398
r_mcbond_it	2.825
r_mcbond_other	2.787
r_angle_refined_deg	1.552
r_angle_other_deg	0.863
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2689
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing