5OG5 | pdb_00005og5

Cu nitrite reductase serial data at varying temperatures RT 0.21MGy

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5I6K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	100 mM sodium citrate at pH 5.0 and ~1.7 M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.252	α = 90
b = 96.252	β = 90
c = 96.252	γ = 90

Symmetry
Space Group	P 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	DECTRIS PILATUS 6M		2015-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.8	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	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	1.82	48.13	99.5	0.094	0.99	4.9	3.3		26363

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.87	99.7		0.462	0.58	1.5	3.2

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	5I6K	1.82	48.13	25397	1302	99.19	0.17544	0.17369	0.18	0.20946	0.21	RANDOM	22.287

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	36.929
r_dihedral_angle_4_deg	20.008
r_dihedral_angle_3_deg	14.32
r_dihedral_angle_1_deg	7.551
r_long_range_B_refined	5.816
r_long_range_B_other	5.804
r_scangle_other	3.545
r_mcangle_it	2.321
r_mcangle_other	2.321
r_scbond_it	2.291
r_scbond_other	2.199
r_angle_refined_deg	1.717
r_mcbond_it	1.5
r_mcbond_other	1.5
r_angle_other_deg	1.02
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_gen_planes_other	0.009
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2566
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data collection
XDS	data reduction
Aimless	data scaling
REFMAC	phasing