5G5G | pdb_00005g5g

Escherichia coli Periplasmic Aldehyde Oxidase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RM6	PDB ENTRIES 1RM6, 1T3Q, 1FFU, 1FFV
experimental model	PDB	1T3Q	PDB ENTRIES 1RM6, 1T3Q, 1FFU, 1FFV
experimental model	PDB	1FFU	PDB ENTRIES 1RM6, 1T3Q, 1FFU, 1FFV
experimental model	PDB	1FFV	PDB ENTRIES 1RM6, 1T3Q, 1FFU, 1FFV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		PEG 3350, AMMONIUM IODIDE, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.681	α = 90
b = 78.342	β = 99.69
c = 151.909	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS PILATUS 6M		2014-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1		SOLEIL	PROXIMA 1

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	1.7	48.32	98.5	0.11	9.69	4.4		137342		1.9

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	1.7	1.73	99		0.86	1.9	4.4

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	PDB ENTRIES 1RM6, 1T3Q, 1FFU, 1FFV	1.7	48.32	130506	6835	98.52	0.13988	0.13848	0.15	0.16745	0.18	RANDOM	20.871

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]
-0.23		0.1	-0.27		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.767
r_dihedral_angle_4_deg	17.756
r_dihedral_angle_3_deg	12.103
r_dihedral_angle_1_deg	6.24
r_angle_refined_deg	2.046
r_scbond_it	1.483
r_mcangle_it	1.426
r_angle_other_deg	1.299
r_mcbond_it	0.912
r_mcbond_other	0.874
r_chiral_restr	0.103
r_bond_refined_d	0.02
r_gen_planes_refined	0.02
r_gen_planes_other	0.015
r_bond_other_d	0.007
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9136
Nucleic Acid Atoms
Solvent Atoms	981
Heterogen Atoms	188

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing