4N4N | pdb_00004n4n

Nitrosomonas europea HAO

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FGJ	PDB ENTRY 1FGJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH UNDER OIL	7.5	293	42% v/v PEG400, 50 mM potassium nitrate, 100 mM MES/NaOH, pH 7.5, MICROBATCH UNDER OIL, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.72	α = 90
b = 141.97	β = 90
c = 106.72	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	PSI PILATUS 6M	two horizontal deflecting and one vertical deflecting X-ray mirror	2012-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	0.9786	PETRA III, DESY	P11

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	2.2	50.4	99.5	0.102	13.6	5.6	98124	98124

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	2.2	2.3	99.3		0.588

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1FGJ	2.2	50.4	98124	98124	10263	99.97	0.18246	0.18246	0.17928	0.18	0.21273	0.21	RANDOM	29.017

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]
-2.15			0.26		1.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.164
r_dihedral_angle_4_deg	17.906
r_dihedral_angle_3_deg	14.63
r_dihedral_angle_1_deg	5.055
r_scangle_it	1.124
r_angle_refined_deg	1.025
r_scbond_it	0.723
r_mcangle_it	0.536
r_mcbond_it	0.283
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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	13309
Nucleic Acid Atoms
Solvent Atoms	1094
Heterogen Atoms	1038

Software

Software
Software Name	Purpose
HEIDI	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling