Experiment: 4ZXV

Streptomyces peucetius nitrososynthase DnmZ in ligand-free state

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MXL	PDB entry 3MXL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.3	298	0.1 M glycine, 0.12 M ammonium sulfate, 12% PEG2000

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.836	α = 90
b = 134.491	β = 90
c = 142.925	γ = 90

Symmetry
Space Group	P 21 21 21

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		2011-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.95370	SSRL	BL12-2

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	3	50	97.8	0.063	17.5	3.2		38251			97.065

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	3	3.11	95.3		0.465	2.3	3.1	3691

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 entry 3MXL	3	48.97	36262	1937	97.63	0.2131	0.2102	0.2056	0.265	0.2644	RANDOM	100.166

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.218
r_dihedral_angle_4_deg	16.801
r_dihedral_angle_3_deg	16.618
r_dihedral_angle_1_deg	5.324
r_angle_refined_deg	1.496
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11438
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
Blu-Ice	data collection
HKL-2000	data reduction