5G5H | pdb_00005g5h

Escherichia coli Periplasmic Aldehyde Oxidase R440H mutant

X-RAY DIFFRACTION

---

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	48.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.839	α = 90
b = 78.263	β = 99.93
c = 151.732	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 2M		2015-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	2.3	48.27	98	0.21	8.7	7.2		55360		1.81

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	2.3	2.37	84.2		0.83	1.81	4.9

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	2.3	48.27	52541	2811	97.95	0.16664	0.16378	0.17	0.2196	0.22	RANDOM	27.324

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]
-0.3		0.01	-0.15		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.75
r_dihedral_angle_4_deg	15.425
r_dihedral_angle_3_deg	12.918
r_dihedral_angle_1_deg	6.429
r_long_range_B_refined	4.434
r_long_range_B_other	4.434
r_scangle_other	2.091
r_angle_refined_deg	1.857
r_mcangle_it	1.525
r_mcangle_other	1.525
r_scbond_it	1.286
r_scbond_other	1.286
r_angle_other_deg	1.204
r_mcbond_it	0.918
r_mcbond_other	0.917
r_chiral_restr	0.073
r_bond_refined_d	0.023
r_gen_planes_refined	0.022
r_bond_other_d	0.01
r_gen_planes_other	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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9104
Nucleic Acid Atoms
Solvent Atoms	661
Heterogen Atoms	173

Software

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