2PP9 | pdb_00002pp9

Nitrate bound wild type oxidized AfNiR

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
2.05	39.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.91	α = 90
b = 102.084	β = 90
c = 145.83	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	IMAGE PLATE	MAR scanner 345 mm plate	mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	1.8	30		0.088		5		85408

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	1.8	1.86			0.428		5

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	30	76833	4029	95.14	0.17071	0.16941	0.1671	0.19529	0.1927	RANDOM	21.364

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]
2.06			-0.69		-1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.282
r_dihedral_angle_4_deg	21.041
r_dihedral_angle_3_deg	12.604
r_dihedral_angle_1_deg	7.041
r_scangle_it	2.66
r_scbond_it	1.757
r_angle_refined_deg	1.33
r_mcangle_it	1.039
r_mcbond_it	0.696
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.226
r_nbd_refined	0.189
r_xyhbond_nbd_refined	0.143
r_symmetry_hbond_refined	0.115
r_chiral_restr	0.089
r_metal_ion_refined	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7687
Nucleic Acid Atoms
Solvent Atoms	951
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing