2AT5 | pdb_00002at5

1.22 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) Deuteroporphyrin IX Complexed With Nitric Oxide at pH 5.6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X8O	PDB entry 1X8O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	300	ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K

Crystal Properties
Matthews coefficient	Solvent content
1.61	22.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.21	α = 90
b = 42.666	β = 94.27
c = 53.005	γ = 90

Symmetry
Space Group	C 1 2 1

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	Bent conical Si-mirror (Rh coating)	2003-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.22	20.38	95.8	0.06	0.06	24.3	5.93		44702			11.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.22	1.26	95.8	96.1	0.18	0.18	10.6	5.74	4462

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	FOURIER SYNTHESIS	FREE R	PDB entry 1X8O	1.22	20.38	44644	44644	2233	95.68	0.119	0.118	0.118	0.1196	0.148	0.1485	RANDOM	7.583

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]
0.15			0.06		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.03
r_dihedral_angle_3_deg	12.556
r_dihedral_angle_4_deg	9.032
r_sphericity_free	7.737
r_dihedral_angle_1_deg	7.387
r_scangle_it	3.809
r_scbond_it	3.13
r_sphericity_bonded	2.867
r_mcangle_it	2.095
r_mcbond_it	1.738
r_angle_refined_deg	1.674
r_rigid_bond_restr	1.423
r_angle_other_deg	0.927
r_mcbond_other	0.608
r_nbd_refined	0.47
r_symmetry_vdw_other	0.252
r_nbd_other	0.23
r_metal_ion_refined	0.225
r_symmetry_vdw_refined	0.212
r_nbtor_refined	0.192
r_symmetry_hbond_refined	0.17
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.109
r_nbtor_other	0.089
r_xyhbond_nbd_other	0.016
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1714
Nucleic Acid Atoms
Solvent Atoms	307
Heterogen Atoms	85

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data scaling