5I6K | pdb_00005i6k

Crystal Structure of Copper Nitrite Reductase at 100K after 0.69 MGy

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BWI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	4.5	298	1.7 M Ammonium Sulphate, 0.1 M Sodium Acetate pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.287	α = 90
b = 95.287	β = 90
c = 95.287	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	100	PIXEL	DECTRIS PILATUS3 6M		2013-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.07	42.61	96.7	0.048	0.054	0.026	0.999	13.4	3.9		121734

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.07	1.09	87.9		0.889	1.075	0.592	0.541		2.7	5443

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	2BWI	1.07	42.61	115651	6069	96.31	0.1396	0.1383	0.1387	0.1623	0.1622	RANDOM	14.026

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	35.206
r_sphericity_free	29.044
r_dihedral_angle_4_deg	19.196
r_dihedral_angle_3_deg	12.332
r_sphericity_bonded	8.242
r_dihedral_angle_1_deg	8.164
r_rigid_bond_restr	2.102
r_mcangle_it	1.794
r_angle_refined_deg	1.771
r_mcbond_it	1.588
r_mcbond_other	1.576
r_angle_other_deg	1.017
r_chiral_restr	0.114
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2581
Nucleic Acid Atoms
Solvent Atoms	382
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing