2IVD

Structure of protoporphyrinogen oxidase from Myxococcus xanthus with acifluorfen

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		0.1M TRIS/HCL PH 7.5, 1.5M AMMONIUM SULPHATE, 20% GLYCEROL, 1% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
3.66	66.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.918	α = 90
b = 148.918	β = 90
c = 131.924	γ = 90

Symmetry
Space Group	P 4 21 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	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1		SRS	PX14.1

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	2.3	49.4	75.2	0.07	8.7	2.5		55419		1

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	2.38	46.7		0.53	1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	OTHER	THROUGHOUT	2.3	49.39	55419	1748	86.3	0.235	0.234	0.283	RANDOM	33.82

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]
0.02			0.02		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.041
r_dihedral_angle_4_deg	20.545
r_dihedral_angle_3_deg	18.733
r_dihedral_angle_1_deg	6.564
r_scangle_it	1.835
r_angle_refined_deg	1.487
r_scbond_it	1.103
r_mcangle_it	0.918
r_mcbond_it	0.519
r_nbtor_refined	0.296
r_symmetry_vdw_refined	0.258
r_nbd_refined	0.193
r_symmetry_hbond_refined	0.193
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.128
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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	6632
Nucleic Acid Atoms
Solvent Atoms	288
Heterogen Atoms	209

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling