2AT6

1.22 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) Deuteroporphyrin IX Complexed With Water 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	1X8Q	PDB entry 1X8Q

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
1.56	20.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.288	α = 90
b = 42.699	β = 94.35
c = 52.979	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	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	21.35	95.7	0.07	0.07	15.3	6.19		44684			15.1

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	94	93.9	0.31	0.31	3.4	6.02	4353

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R	PDB entry 1X8Q	1.22	20.38	44670	44670	2233	95.64	0.134	0.134	0.133	0.167	RANDOM	10.368

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]
0.71		-0.27	0.06		-0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.331
r_dihedral_angle_3_deg	13.795
r_dihedral_angle_4_deg	9.112
r_sphericity_free	8.772
r_dihedral_angle_1_deg	7.355
r_scangle_it	4.282
r_sphericity_bonded	3.636
r_scbond_it	3.48
r_mcangle_it	2.328
r_mcbond_it	1.908
r_angle_refined_deg	1.76
r_rigid_bond_restr	1.67
r_angle_other_deg	0.94
r_mcbond_other	0.705
r_nbd_refined	0.494
r_symmetry_vdw_refined	0.258
r_nbd_other	0.239
r_symmetry_vdw_other	0.193
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.155
r_symmetry_hbond_refined	0.151
r_chiral_restr	0.112
r_nbtor_other	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1769
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	78

Software

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