3C77

1.08 A crystal structure of nitrophorin 4 from Rhodnius prolixus containing FE(III) deuteroporphyrin ix complexed with ammonia at ph 7.5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X8P	PDB ENTRY 1X8P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	300	AMMONIUM PHOSPHATE, pH 7.50, temperature 300.0K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
1.64	24.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.156	α = 90
b = 42.745	β = 94.03
c = 52.821	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)	2003-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		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	1.07	21.8	94.9	0.06	0.06	16.1	6.68		65307			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)
	1.07	1.11	91		0.18	0.18	3.6	6.06

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R	PDB ENTRY 1X8P	1.08	21.8	63622	3207	95.1	0.137	0.137	0.162	RANDOM	9.59

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]
0.24		-0.01	-0.45		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.451
r_dihedral_angle_3_deg	12.182
r_dihedral_angle_4_deg	8.623
r_sphericity_free	8.149
r_dihedral_angle_1_deg	7.343
r_scangle_it	3.809
r_sphericity_bonded	3.483
r_scbond_it	3.142
r_mcangle_it	2.355
r_mcbond_it	1.915
r_angle_refined_deg	1.726
r_rigid_bond_restr	1.508
r_angle_other_deg	0.856
r_mcbond_other	0.715
r_nbd_refined	0.42
r_nbd_other	0.2
r_nbtor_refined	0.186
r_symmetry_vdw_other	0.172
r_xyhbond_nbd_refined	0.152
r_symmetry_hbond_refined	0.13
r_chiral_restr	0.103
r_nbtor_other	0.087
r_symmetry_vdw_refined	0.064
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_metal_ion_refined	0.003
r_bond_other_d	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1682
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	79

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data scaling