2PPA | pdb_00002ppa

Anaerobically manipulated wild type oxidized AfNiR bound to nitrous oxide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	6-11% PEG 4000, 100mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.65	α = 90
b = 101.623	β = 90
c = 146.042	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	CCD	ADSC QUANTUM 4		2004-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-3	0.97	SSRL	BL11-3

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	1.69	30		0.127		4.8		100417

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	1.69	1.76			0.378		4.7

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.69	30	91791	4834	95.61	0.19281	0.19119	0.22361	RANDOM	23.638

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]
2.46			-0.34		-2.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.003
r_dihedral_angle_4_deg	19.81
r_dihedral_angle_3_deg	12.321
r_dihedral_angle_1_deg	6.853
r_scangle_it	2.539
r_scbond_it	1.642
r_angle_refined_deg	1.308
r_mcangle_it	0.974
r_mcbond_it	0.611
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.003
r_dihedral_angle_4_deg	19.81
r_dihedral_angle_3_deg	12.321
r_dihedral_angle_1_deg	6.853
r_scangle_it	2.539
r_scbond_it	1.642
r_angle_refined_deg	1.308
r_mcangle_it	0.974
r_mcbond_it	0.611
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.198
r_nbd_refined	0.191
r_symmetry_hbond_refined	0.131
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.087
r_metal_ion_refined	0.02
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7687
Nucleic Acid Atoms
Solvent Atoms	776
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.